Query 040593
Match_columns 342
No_of_seqs 92 out of 94
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 09:53:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040593.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040593hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484 Transcription factor P 99.8 6.4E-21 1.4E-25 161.4 3.0 68 260-327 10-77 (125)
2 KOG2251 Homeobox transcription 99.8 4.2E-19 9E-24 164.0 5.4 67 258-324 27-94 (228)
3 KOG0494 Transcription factor C 99.7 3.5E-18 7.7E-23 162.2 5.1 63 267-329 141-203 (332)
4 PF00046 Homeobox: Homeobox do 99.6 2.2E-16 4.8E-21 112.8 4.8 55 269-323 2-56 (57)
5 smart00389 HOX Homeodomain. DN 99.6 3.1E-15 6.8E-20 105.4 6.1 54 270-323 3-56 (56)
6 KOG0489 Transcription factor z 99.6 8E-16 1.7E-20 142.3 3.9 58 267-324 159-216 (261)
7 cd00086 homeodomain Homeodomai 99.5 8.9E-15 1.9E-19 103.2 6.0 56 269-324 2-57 (59)
8 KOG0490 Transcription factor, 99.5 2E-15 4.2E-20 130.5 1.9 61 266-326 59-119 (235)
9 KOG0488 Transcription factor B 99.5 6.2E-15 1.3E-19 140.4 4.9 58 266-323 171-228 (309)
10 TIGR01565 homeo_ZF_HD homeobox 99.5 8.2E-15 1.8E-19 110.9 4.5 52 268-319 2-57 (58)
11 KOG0843 Transcription factor E 99.5 1.9E-14 4.1E-19 130.7 4.0 58 267-324 102-159 (197)
12 KOG0486 Transcription factor P 99.5 2.6E-14 5.6E-19 138.2 2.8 62 265-326 110-171 (351)
13 KOG4577 Transcription factor L 99.4 4.6E-14 9.9E-19 136.1 3.5 62 265-326 165-226 (383)
14 KOG0487 Transcription factor A 99.4 7.2E-14 1.6E-18 134.1 3.3 60 268-327 236-295 (308)
15 COG5576 Homeodomain-containing 99.3 1.1E-12 2.4E-17 115.2 4.3 62 267-328 51-112 (156)
16 KOG0849 Transcription factor P 99.3 1.1E-12 2.4E-17 126.6 4.6 56 268-323 177-232 (354)
17 KOG0844 Transcription factor E 99.3 1.2E-12 2.6E-17 127.2 2.4 68 257-324 171-238 (408)
18 KOG0493 Transcription factor E 99.2 3.9E-12 8.4E-17 121.7 4.1 59 268-326 247-305 (342)
19 KOG0492 Transcription factor M 99.2 4.1E-12 8.8E-17 118.1 3.1 57 267-323 144-200 (246)
20 KOG0483 Transcription factor H 99.2 1.1E-11 2.4E-16 112.8 4.8 59 267-325 50-108 (198)
21 KOG0485 Transcription factor N 99.2 9.6E-12 2.1E-16 116.5 2.8 56 268-323 105-160 (268)
22 KOG0842 Transcription factor t 99.2 1.2E-11 2.6E-16 119.0 3.5 60 264-323 150-209 (307)
23 KOG0848 Transcription factor C 99.1 2.1E-11 4.6E-16 116.6 2.0 53 271-323 203-255 (317)
24 KOG0850 Transcription factor D 99.1 5.9E-11 1.3E-15 111.2 4.4 56 268-323 123-178 (245)
25 KOG0847 Transcription factor, 99.0 1.1E-10 2.4E-15 109.7 3.3 58 267-324 167-224 (288)
26 KOG0491 Transcription factor B 99.0 1.6E-10 3.5E-15 104.7 1.5 58 267-324 100-157 (194)
27 KOG3802 Transcription factor O 98.9 7.2E-10 1.6E-14 109.8 3.4 63 266-328 293-355 (398)
28 KOG0490 Transcription factor, 98.6 2.3E-08 5E-13 86.7 3.4 139 169-325 66-211 (235)
29 PF05920 Homeobox_KN: Homeobox 98.0 3.6E-06 7.9E-11 59.5 2.9 34 288-321 7-40 (40)
30 KOG0775 Transcription factor S 98.0 5.5E-06 1.2E-10 80.0 4.5 57 267-323 173-232 (304)
31 KOG2252 CCAAT displacement pro 97.8 2.1E-05 4.5E-10 81.3 5.3 52 270-321 423-474 (558)
32 KOG1168 Transcription factor A 97.7 1E-05 2.2E-10 79.3 0.3 58 266-323 308-365 (385)
33 KOG1146 Homeobox protein [Gene 97.2 0.00026 5.7E-09 79.2 3.8 59 267-325 903-961 (1406)
34 KOG0774 Transcription factor P 97.2 0.00027 5.8E-09 68.7 3.2 58 266-323 187-247 (334)
35 PF11569 Homez: Homeodomain le 96.1 0.0052 1.1E-07 47.2 3.0 44 278-321 9-52 (56)
36 PF04967 HTH_10: HTH DNA bindi 95.8 0.019 4.2E-07 43.1 4.9 41 171-211 2-46 (53)
37 KOG3623 Homeobox transcription 95.8 0.014 3E-07 63.3 5.7 63 271-335 561-623 (1007)
38 COG3413 Predicted DNA binding 95.2 0.03 6.6E-07 50.2 4.8 43 169-211 155-201 (215)
39 PF02796 HTH_7: Helix-turn-hel 95.1 0.028 6E-07 39.7 3.3 44 166-212 2-45 (45)
40 KOG0773 Transcription factor M 94.9 0.014 3.1E-07 55.4 2.1 61 265-325 237-300 (342)
41 PF04931 DNA_pol_phi: DNA poly 93.3 0.26 5.6E-06 52.5 7.7 15 120-134 702-716 (784)
42 PF00046 Homeobox: Homeobox do 90.6 0.43 9.3E-06 34.0 3.9 43 169-211 6-50 (57)
43 smart00389 HOX Homeodomain. DN 90.0 0.47 1E-05 33.3 3.6 42 170-211 7-50 (56)
44 PF04931 DNA_pol_phi: DNA poly 89.9 0.29 6.4E-06 52.1 3.6 11 87-97 623-633 (784)
45 TIGR01565 homeo_ZF_HD homeobox 89.5 0.33 7.1E-06 37.3 2.7 44 169-212 7-56 (58)
46 KOG1832 HIV-1 Vpr-binding prot 88.0 0.16 3.5E-06 56.7 0.2 12 106-117 1447-1458(1516)
47 cd00569 HTH_Hin_like Helix-tur 87.9 1.6 3.4E-05 25.5 4.4 31 176-209 12-42 (42)
48 PF13518 HTH_28: Helix-turn-he 86.6 1.2 2.5E-05 30.8 3.8 30 180-212 7-36 (52)
49 PF04218 CENP-B_N: CENP-B N-te 86.3 1.5 3.2E-05 32.3 4.4 46 269-319 2-47 (53)
50 PF13551 HTH_29: Winged helix- 86.0 4.3 9.3E-05 31.4 7.1 95 180-316 6-109 (112)
51 cd00086 homeodomain Homeodomai 84.4 1.8 3.9E-05 30.2 4.0 43 169-211 6-50 (59)
52 PF01527 HTH_Tnp_1: Transposas 82.7 2.1 4.6E-05 31.7 3.9 35 175-212 13-47 (76)
53 COG5414 TATA-binding protein-a 80.9 2.9 6.4E-05 42.1 5.2 105 100-204 257-386 (392)
54 PF04218 CENP-B_N: CENP-B N-te 80.5 2.1 4.6E-05 31.5 3.2 40 169-211 6-45 (53)
55 PF09339 HTH_IclR: IclR helix- 79.5 2.4 5.3E-05 30.2 3.2 33 178-210 8-40 (52)
56 PF13936 HTH_38: Helix-turn-he 78.2 2.4 5.1E-05 30.0 2.7 36 173-211 8-43 (44)
57 PF04760 IF2_N: Translation in 76.1 2.1 4.6E-05 30.9 2.1 23 188-210 3-25 (54)
58 PF08279 HTH_11: HTH domain; 74.7 7.3 0.00016 27.5 4.5 33 178-210 5-37 (55)
59 cd06171 Sigma70_r4 Sigma70, re 73.8 5.2 0.00011 26.1 3.4 45 272-321 9-53 (55)
60 PRK13558 bacterio-opsin activa 73.6 5.3 0.00012 40.5 4.9 43 169-211 607-653 (665)
61 PRK06596 RNA polymerase factor 72.9 14 0.00031 34.8 7.3 123 174-316 138-270 (284)
62 PF09012 FeoC: FeoC like trans 72.6 4.5 9.8E-05 30.5 3.2 27 184-210 10-36 (69)
63 PF13412 HTH_24: Winged helix- 71.5 9.6 0.00021 26.4 4.4 35 174-210 5-39 (48)
64 KOG2038 CAATT-binding transcri 71.4 1.5 3.2E-05 48.7 0.4 9 112-120 881-889 (988)
65 PF13384 HTH_23: Homeodomain-l 71.0 4.7 0.0001 27.9 2.8 25 188-212 17-41 (50)
66 TIGR01764 excise DNA binding d 70.8 5.1 0.00011 26.7 2.8 24 189-212 2-25 (49)
67 TIGR02885 spore_sigF RNA polym 70.5 15 0.00032 32.8 6.5 111 187-317 112-222 (231)
68 cd00569 HTH_Hin_like Helix-tur 70.1 14 0.0003 21.3 4.4 40 271-315 3-42 (42)
69 smart00421 HTH_LUXR helix_turn 69.7 12 0.00027 25.0 4.5 48 273-326 3-50 (58)
70 PRK07500 rpoH2 RNA polymerase 67.7 26 0.00056 33.3 7.8 128 173-320 129-271 (289)
71 cd00131 PAX Paired Box domain 67.6 74 0.0016 27.1 9.8 36 174-212 22-57 (128)
72 PF13443 HTH_26: Cro/C1-type H 67.5 6.5 0.00014 28.2 3.0 27 186-212 8-34 (63)
73 PRK10403 transcriptional regul 67.4 7.8 0.00017 31.5 3.7 49 273-327 153-201 (215)
74 smart00530 HTH_XRE Helix-turn- 67.1 14 0.00029 23.3 4.2 26 187-212 9-34 (56)
75 PRK10360 DNA-binding transcrip 67.0 8.1 0.00018 31.6 3.8 50 272-327 136-185 (196)
76 PF12802 MarR_2: MarR family; 66.5 16 0.00034 25.9 4.8 40 171-210 4-43 (62)
77 smart00342 HTH_ARAC helix_turn 66.0 15 0.00033 26.1 4.6 39 171-211 35-74 (84)
78 smart00346 HTH_ICLR helix_turn 65.5 12 0.00026 28.4 4.2 34 178-211 10-43 (91)
79 PF00440 TetR_N: Bacterial reg 65.5 12 0.00027 26.0 4.0 34 178-211 6-39 (47)
80 TIGR02844 spore_III_D sporulat 65.4 16 0.00034 29.7 5.0 37 175-214 9-45 (80)
81 smart00344 HTH_ASNC helix_turn 64.3 12 0.00026 29.5 4.1 35 176-211 6-40 (108)
82 PF04967 HTH_10: HTH DNA bindi 64.2 11 0.00023 28.5 3.7 42 274-315 1-44 (53)
83 PF12324 HTH_15: Helix-turn-he 64.2 9.7 0.00021 31.2 3.6 43 169-212 20-62 (77)
84 smart00550 Zalpha Z-DNA-bindin 63.5 17 0.00038 27.6 4.8 34 177-210 10-44 (68)
85 COG5593 Nucleic-acid-binding p 63.1 8.9 0.00019 41.6 4.1 26 79-104 680-709 (821)
86 cd04762 HTH_MerR-trunc Helix-T 62.6 8.7 0.00019 25.2 2.6 22 190-211 2-23 (49)
87 PRK05572 sporulation sigma fac 62.0 31 0.00067 31.5 6.9 43 270-317 199-241 (252)
88 cd06170 LuxR_C_like C-terminal 60.9 15 0.00033 24.8 3.7 47 274-326 1-47 (57)
89 PF06056 Terminase_5: Putative 60.6 18 0.00039 27.4 4.3 35 177-213 4-38 (58)
90 PF13404 HTH_AsnC-type: AsnC-t 60.0 20 0.00042 25.5 4.2 32 177-209 7-38 (42)
91 PF04545 Sigma70_r4: Sigma-70, 60.0 18 0.00038 25.4 4.0 41 273-318 4-44 (50)
92 PF00196 GerE: Bacterial regul 60.0 10 0.00022 27.4 2.8 50 272-327 2-51 (58)
93 PF01325 Fe_dep_repress: Iron 59.9 22 0.00047 26.8 4.7 27 185-211 19-45 (60)
94 TIGR02980 SigBFG RNA polymeras 59.8 30 0.00066 30.7 6.3 43 272-319 177-219 (227)
95 TIGR02392 rpoH_proteo alternat 59.3 50 0.0011 30.7 7.9 126 175-321 126-263 (270)
96 TIGR03070 couple_hipB transcri 59.3 14 0.00031 25.2 3.4 28 185-212 12-39 (58)
97 COG1427 Predicted periplasmic 58.7 7 0.00015 37.9 2.3 50 275-325 180-229 (252)
98 cd00090 HTH_ARSR Arsenical Res 58.6 24 0.00051 24.3 4.4 37 172-211 7-43 (78)
99 smart00420 HTH_DEOR helix_turn 58.0 26 0.00057 23.4 4.4 24 188-211 14-37 (53)
100 TIGR02937 sigma70-ECF RNA poly 57.9 20 0.00044 27.6 4.4 39 169-210 110-148 (158)
101 PF01978 TrmB: Sugar-specific 57.7 22 0.00048 26.3 4.3 40 170-211 6-45 (68)
102 PF04539 Sigma70_r3: Sigma-70 57.1 28 0.00061 26.1 4.9 28 183-211 16-43 (78)
103 cd00093 HTH_XRE Helix-turn-hel 57.1 25 0.00053 22.3 4.0 27 186-212 10-36 (58)
104 PF09026 CENP-B_dimeris: Centr 56.9 3.6 7.7E-05 35.3 0.0 7 161-167 36-42 (101)
105 KOG1446 Histone H3 (Lys4) meth 56.9 3.9 8.4E-05 40.8 0.2 35 7-41 70-108 (311)
106 PF01047 MarR: MarR family; I 56.4 27 0.00058 24.7 4.5 35 174-210 5-39 (59)
107 PRK10014 DNA-binding transcrip 56.4 14 0.00029 33.7 3.6 29 185-213 3-31 (342)
108 PF00356 LacI: Bacterial regul 56.1 17 0.00036 26.5 3.3 24 190-213 1-24 (46)
109 PF12728 HTH_17: Helix-turn-he 55.8 13 0.00029 26.0 2.7 24 189-212 2-25 (51)
110 PRK09413 IS2 repressor TnpA; R 55.5 18 0.0004 30.0 4.0 35 175-212 19-53 (121)
111 TIGR02431 pcaR_pcaU beta-ketoa 55.3 17 0.00036 33.1 4.0 32 180-211 16-47 (248)
112 KOG1146 Homeobox protein [Gene 55.3 4.1 9E-05 47.2 0.2 65 265-329 442-506 (1406)
113 PHA01976 helix-turn-helix prot 55.1 26 0.00056 25.4 4.3 27 185-211 12-38 (67)
114 PF07278 DUF1441: Protein of u 54.9 13 0.00029 33.6 3.2 26 188-213 1-26 (152)
115 PRK09210 RNA polymerase sigma 54.4 49 0.0011 32.6 7.4 44 272-316 304-347 (367)
116 PRK14987 gluconate operon tran 54.3 13 0.00029 33.8 3.2 28 186-213 3-30 (331)
117 KOG2038 CAATT-binding transcri 53.8 12 0.00026 41.8 3.3 6 127-132 903-908 (988)
118 PF13443 HTH_26: Cro/C1-type H 53.4 9.5 0.00021 27.4 1.7 25 296-320 12-36 (63)
119 PRK07122 RNA polymerase sigma 53.0 34 0.00074 32.0 5.7 45 272-321 214-258 (264)
120 COG1522 Lrp Transcriptional re 52.8 23 0.0005 29.3 4.2 34 176-211 12-45 (154)
121 PF01381 HTH_3: Helix-turn-hel 52.8 34 0.00073 23.8 4.4 26 186-211 7-32 (55)
122 PRK11569 transcriptional repre 51.9 20 0.00044 33.3 4.1 32 179-210 34-65 (274)
123 PRK15369 two component system 51.9 27 0.00058 28.0 4.2 49 273-327 149-197 (211)
124 smart00421 HTH_LUXR helix_turn 51.8 40 0.00086 22.4 4.5 27 182-211 15-41 (58)
125 PRK09935 transcriptional regul 51.0 22 0.00049 29.0 3.8 51 272-328 148-198 (210)
126 COG0568 RpoD DNA-directed RNA 50.8 52 0.0011 33.2 7.0 128 175-323 191-328 (342)
127 PF01527 HTH_Tnp_1: Transposas 50.8 13 0.00029 27.4 2.2 46 270-319 3-48 (76)
128 PRK09492 treR trehalose repres 50.7 17 0.00037 32.6 3.3 28 186-213 2-29 (315)
129 PF05930 Phage_AlpA: Prophage 50.6 12 0.00027 26.9 1.9 25 187-211 2-26 (51)
130 PF05764 YL1: YL1 nuclear prot 50.5 24 0.00051 33.2 4.3 7 272-278 183-189 (240)
131 PF05225 HTH_psq: helix-turn-h 50.2 36 0.00077 24.5 4.2 33 180-214 10-42 (45)
132 PHA00542 putative Cro-like pro 50.2 37 0.00081 26.7 4.8 26 187-212 30-55 (82)
133 PF05044 HPD: Homeo-prospero d 50.2 9.9 0.00022 34.8 1.7 48 273-320 2-52 (158)
134 TIGR03879 near_KaiC_dom probab 50.0 7.9 0.00017 31.1 0.9 39 282-320 20-58 (73)
135 PRK05657 RNA polymerase sigma 49.3 76 0.0016 30.9 7.6 116 187-321 188-309 (325)
136 PRK08215 sporulation sigma fac 49.2 69 0.0015 29.4 7.0 42 271-317 207-248 (258)
137 TIGR00498 lexA SOS regulatory 49.0 28 0.00062 30.6 4.3 41 170-210 4-48 (199)
138 COG1309 AcrR Transcriptional r 49.0 32 0.0007 26.4 4.2 34 179-212 23-56 (201)
139 smart00354 HTH_LACI helix_turn 48.0 24 0.00052 26.7 3.3 25 189-213 1-25 (70)
140 TIGR02479 FliA_WhiG RNA polyme 47.4 49 0.0011 29.5 5.6 44 272-320 174-217 (224)
141 cd04761 HTH_MerR-SF Helix-Turn 46.7 19 0.00041 24.4 2.3 22 297-318 3-24 (49)
142 smart00342 HTH_ARAC helix_turn 46.5 22 0.00048 25.3 2.8 24 188-211 1-24 (84)
143 PRK11179 DNA-binding transcrip 46.5 33 0.00071 29.4 4.2 35 176-211 12-46 (153)
144 PHA00675 hypothetical protein 46.3 36 0.00077 28.2 4.1 41 167-210 20-61 (78)
145 cd04762 HTH_MerR-trunc Helix-T 46.2 20 0.00044 23.4 2.4 24 297-320 3-26 (49)
146 PRK10651 transcriptional regul 45.6 30 0.00065 28.2 3.7 49 273-327 155-203 (216)
147 PRK10100 DNA-binding transcrip 45.2 24 0.00052 32.1 3.4 49 273-327 155-203 (216)
148 cd07377 WHTH_GntR Winged helix 44.7 55 0.0012 22.8 4.5 29 183-211 20-48 (66)
149 smart00351 PAX Paired Box doma 44.6 40 0.00087 28.4 4.4 36 174-212 22-57 (125)
150 PRK09526 lacI lac repressor; R 44.4 26 0.00057 31.9 3.5 28 186-213 3-30 (342)
151 PF14549 P22_Cro: DNA-binding 43.8 7.7 0.00017 29.8 0.0 27 297-329 12-38 (60)
152 PF03374 ANT: Phage antirepres 43.4 21 0.00046 28.6 2.5 26 187-212 23-48 (111)
153 TIGR00122 birA_repr_reg BirA b 43.4 46 0.001 24.7 4.1 33 177-211 4-36 (69)
154 smart00345 HTH_GNTR helix_turn 43.4 58 0.0013 22.2 4.4 23 188-210 19-42 (60)
155 PRK00215 LexA repressor; Valid 43.0 41 0.00088 29.7 4.4 30 182-211 17-47 (205)
156 PRK10163 DNA-binding transcrip 42.8 35 0.00076 31.8 4.1 32 179-210 31-62 (271)
157 PRK10072 putative transcriptio 42.6 21 0.00045 29.7 2.3 41 273-320 32-72 (96)
158 TIGR02944 suf_reg_Xantho FeS a 42.6 50 0.0011 27.2 4.6 37 175-211 12-48 (130)
159 PHA01083 hypothetical protein 42.2 28 0.00062 31.7 3.3 36 176-211 4-39 (149)
160 PRK09480 slmA division inhibit 41.9 45 0.00099 27.9 4.3 26 185-211 28-53 (194)
161 cd00092 HTH_CRP helix_turn_hel 41.4 50 0.0011 23.4 3.9 26 186-211 23-48 (67)
162 TIGR02405 trehalos_R_Ecol treh 41.1 30 0.00065 31.4 3.3 26 188-213 1-26 (311)
163 PF02796 HTH_7: Helix-turn-hel 40.2 44 0.00095 23.5 3.4 41 271-316 3-43 (45)
164 PHA02591 hypothetical protein; 39.7 29 0.00063 29.0 2.7 32 178-211 51-82 (83)
165 PF13936 HTH_38: Helix-turn-he 39.6 42 0.00092 23.7 3.2 41 271-316 2-42 (44)
166 TIGR02531 yecD_yerC TrpR-relat 39.3 60 0.0013 26.7 4.5 31 178-211 43-73 (88)
167 PF13411 MerR_1: MerR HTH fami 39.2 28 0.0006 25.3 2.4 20 297-316 3-22 (69)
168 KOG3623 Homeobox transcription 39.0 37 0.00079 38.2 4.1 99 186-321 581-680 (1007)
169 PF12844 HTH_19: Helix-turn-he 39.0 39 0.00085 24.2 3.1 25 187-211 11-35 (64)
170 PRK09480 slmA division inhibit 38.9 37 0.00079 28.5 3.3 40 279-319 16-55 (194)
171 PF01381 HTH_3: Helix-turn-hel 38.9 29 0.00063 24.1 2.3 23 297-319 12-34 (55)
172 PRK13239 alkylmercury lyase; P 38.4 61 0.0013 30.6 5.0 42 171-213 20-61 (206)
173 PF08281 Sigma70_r4_2: Sigma-7 38.3 25 0.00053 24.7 1.9 43 274-321 11-53 (54)
174 TIGR02607 antidote_HigA addict 38.3 40 0.00087 25.0 3.1 27 186-212 16-42 (78)
175 TIGR03070 couple_hipB transcri 38.2 30 0.00066 23.6 2.3 23 297-319 18-40 (58)
176 PF13730 HTH_36: Helix-turn-he 38.1 82 0.0018 22.1 4.6 42 273-317 2-48 (55)
177 PRK05901 RNA polymerase sigma 37.9 84 0.0018 33.2 6.4 108 185-314 372-487 (509)
178 PF13384 HTH_23: Homeodomain-l 37.8 31 0.00067 23.8 2.3 26 294-319 17-42 (50)
179 cd06170 LuxR_C_like C-terminal 37.8 89 0.0019 21.0 4.6 22 189-210 16-37 (57)
180 smart00419 HTH_CRP helix_turn_ 37.0 40 0.00086 22.4 2.7 24 188-211 8-31 (48)
181 PRK09975 DNA-binding transcrip 36.9 52 0.0011 28.3 4.0 32 180-211 23-54 (213)
182 PF01022 HTH_5: Bacterial regu 36.9 53 0.0012 23.0 3.4 32 177-210 6-37 (47)
183 PRK06288 RNA polymerase sigma 36.7 81 0.0018 29.2 5.5 44 271-319 210-253 (268)
184 TIGR03541 reg_near_HchA LuxR f 36.5 40 0.00086 30.8 3.4 51 271-327 169-219 (232)
185 PF06056 Terminase_5: Putative 36.2 32 0.00068 26.1 2.3 22 295-316 14-35 (58)
186 PRK09652 RNA polymerase sigma 35.8 42 0.0009 27.6 3.1 43 272-319 127-169 (182)
187 TIGR03826 YvyF flagellar opero 35.6 78 0.0017 28.1 4.9 30 183-212 41-70 (137)
188 PF13518 HTH_28: Helix-turn-he 35.5 37 0.0008 23.2 2.4 25 296-320 14-38 (52)
189 PF13730 HTH_36: Helix-turn-he 35.5 39 0.00083 23.8 2.5 23 189-211 26-48 (55)
190 COG1318 Predicted transcriptio 35.2 54 0.0012 30.8 4.1 43 172-214 43-87 (182)
191 PRK03975 tfx putative transcri 34.8 42 0.00091 29.8 3.2 45 271-321 4-48 (141)
192 PF05285 SDA1: SDA1; InterPro 34.6 26 0.00056 34.3 2.0 18 85-102 67-84 (324)
193 PRK09834 DNA-binding transcrip 34.5 58 0.0012 30.1 4.2 30 181-210 19-48 (263)
194 PF08280 HTH_Mga: M protein tr 34.3 52 0.0011 24.3 3.1 37 276-316 5-41 (59)
195 PRK15090 DNA-binding transcrip 34.2 53 0.0012 30.1 3.9 24 187-210 27-50 (257)
196 PRK04217 hypothetical protein; 34.0 71 0.0015 27.3 4.3 45 272-321 41-85 (110)
197 PRK13413 mpi multiple promoter 33.8 71 0.0015 28.3 4.5 32 179-213 166-197 (200)
198 PRK10870 transcriptional repre 33.8 73 0.0016 28.2 4.5 44 167-210 50-93 (176)
199 PF13463 HTH_27: Winged helix 33.6 78 0.0017 22.6 3.9 31 181-211 11-41 (68)
200 PF01710 HTH_Tnp_IS630: Transp 33.1 57 0.0012 27.1 3.6 29 179-210 12-40 (119)
201 COG2963 Transposase and inacti 33.0 72 0.0016 25.8 4.0 33 176-211 15-48 (116)
202 TIGR02937 sigma70-ECF RNA poly 32.9 52 0.0011 25.4 3.1 44 273-321 110-153 (158)
203 cd01392 HTH_LacI Helix-turn-he 32.9 40 0.00086 23.2 2.2 21 193-213 2-22 (52)
204 COG3413 Predicted DNA binding 32.7 56 0.0012 29.5 3.7 42 273-314 155-198 (215)
205 PF07093 SGT1: SGT1 protein; 32.4 1.2E+02 0.0025 32.1 6.4 20 112-132 472-491 (589)
206 PRK07598 RNA polymerase sigma 32.3 1.1E+02 0.0023 31.6 6.0 120 187-328 277-404 (415)
207 PRK09958 DNA-binding transcrip 31.8 83 0.0018 25.8 4.3 51 272-328 142-192 (204)
208 TIGR03384 betaine_BetI transcr 31.5 1E+02 0.0023 25.6 4.9 39 173-211 13-51 (189)
209 TIGR03613 RutR pyrimidine util 31.1 77 0.0017 27.0 4.1 33 181-213 21-53 (202)
210 PRK13756 tetracycline represso 31.0 79 0.0017 28.6 4.4 39 175-213 7-49 (205)
211 PF10668 Phage_terminase: Phag 30.9 37 0.00081 26.5 1.9 20 296-315 24-43 (60)
212 PRK09726 antitoxin HipB; Provi 30.7 98 0.0021 24.3 4.4 28 185-212 22-49 (88)
213 PF02082 Rrf2: Transcriptional 30.5 82 0.0018 24.3 3.8 36 175-210 11-47 (83)
214 PF02186 TFIIE_beta: TFIIE bet 30.5 80 0.0017 24.6 3.7 32 182-213 14-46 (65)
215 smart00418 HTH_ARSR helix_turn 30.4 77 0.0017 21.3 3.3 26 186-211 8-33 (66)
216 cd04761 HTH_MerR-SF Helix-Turn 30.1 59 0.0013 21.9 2.7 22 190-211 2-23 (49)
217 PRK00767 transcriptional regul 30.1 1.1E+02 0.0023 25.7 4.8 30 182-211 23-52 (197)
218 PRK09483 response regulator; P 30.0 73 0.0016 26.5 3.7 51 272-328 147-197 (217)
219 TIGR02607 antidote_HigA addict 29.9 47 0.001 24.6 2.3 23 297-319 21-43 (78)
220 PF02954 HTH_8: Bacterial regu 29.6 56 0.0012 22.7 2.5 38 171-210 3-40 (42)
221 PF01402 RHH_1: Ribbon-helix-h 29.6 68 0.0015 21.3 2.8 19 190-208 13-31 (39)
222 PF04889 Cwf_Cwc_15: Cwf15/Cwc 29.5 49 0.0011 31.7 2.9 15 19-33 25-39 (244)
223 PF13411 MerR_1: MerR HTH fami 29.5 58 0.0013 23.6 2.7 23 190-212 2-24 (69)
224 PF12728 HTH_17: Helix-turn-he 29.3 51 0.0011 23.0 2.3 24 297-320 4-27 (51)
225 TIGR00738 rrf2_super rrf2 fami 29.3 66 0.0014 26.2 3.3 29 183-211 20-48 (132)
226 PF13560 HTH_31: Helix-turn-he 29.1 91 0.002 22.7 3.7 29 285-313 34-63 (64)
227 PRK10401 DNA-binding transcrip 29.1 61 0.0013 29.8 3.4 26 188-213 1-26 (346)
228 PLN02543 pfkB-type carbohydrat 29.1 1.1E+02 0.0023 32.1 5.4 15 21-35 26-40 (496)
229 TIGR02684 dnstrm_HI1420 probab 28.8 70 0.0015 26.1 3.3 39 178-216 33-72 (89)
230 PRK10430 DNA-binding transcrip 28.3 1.2E+02 0.0026 26.8 4.9 65 273-338 158-230 (239)
231 PHA01976 helix-turn-helix prot 27.8 56 0.0012 23.7 2.4 23 297-319 18-40 (67)
232 COG2150 Predicted regulator of 27.5 46 0.00099 30.9 2.2 23 188-210 41-63 (167)
233 TIGR02850 spore_sigG RNA polym 27.3 3.4E+02 0.0074 24.9 7.8 41 270-315 203-243 (254)
234 PRK00430 fis global DNA-bindin 27.2 2.6E+02 0.0057 23.0 6.4 41 169-211 51-91 (95)
235 KOG2268 Serine/threonine prote 27.2 1.7E+02 0.0036 30.9 6.3 21 117-137 369-389 (465)
236 COG1654 BirA Biotin operon rep 27.2 1.1E+02 0.0023 25.0 4.0 32 177-208 8-39 (79)
237 PRK10703 DNA-binding transcrip 27.1 68 0.0015 29.3 3.3 25 189-213 2-26 (341)
238 cd03022 DsbA_HCCA_Iso DsbA fam 26.9 1E+02 0.0022 25.9 4.1 37 177-213 108-148 (192)
239 TIGR03020 EpsA transcriptional 26.9 78 0.0017 30.1 3.7 50 272-327 189-238 (247)
240 PF02724 CDC45: CDC45-like pro 26.4 45 0.00097 35.6 2.2 15 192-206 224-238 (622)
241 PRK00215 LexA repressor; Valid 26.0 70 0.0015 28.2 3.1 46 274-321 2-51 (205)
242 PF00392 GntR: Bacterial regul 25.9 1.6E+02 0.0035 21.5 4.5 35 176-210 7-46 (64)
243 PRK09975 DNA-binding transcrip 25.8 79 0.0017 27.2 3.3 41 279-320 17-57 (213)
244 PF13542 HTH_Tnp_ISL3: Helix-t 25.7 1E+02 0.0023 21.3 3.3 23 189-211 28-50 (52)
245 PF13560 HTH_31: Helix-turn-he 25.6 63 0.0014 23.5 2.3 25 296-320 16-40 (64)
246 PF13309 HTH_22: HTH domain 25.2 72 0.0016 24.3 2.6 33 178-210 30-64 (64)
247 PRK04217 hypothetical protein; 25.1 1.4E+02 0.003 25.6 4.5 42 167-211 40-81 (110)
248 TIGR02948 SigW_bacill RNA poly 25.1 73 0.0016 26.8 2.9 45 272-321 135-179 (187)
249 PF01399 PCI: PCI domain; Int 24.9 1.6E+02 0.0034 22.3 4.5 34 177-210 49-82 (105)
250 TIGR03830 CxxCG_CxxCG_HTH puta 24.9 2.1E+02 0.0047 23.0 5.5 25 187-211 77-101 (127)
251 PRK11050 manganese transport r 24.7 1.3E+02 0.0028 26.1 4.4 36 175-211 39-74 (152)
252 cd01104 HTH_MlrA-CarA Helix-Tu 24.7 68 0.0015 23.2 2.3 21 297-317 3-23 (68)
253 COG5271 MDN1 AAA ATPase contai 24.7 96 0.0021 39.1 4.5 82 75-165 3844-3958(4600)
254 COG3415 Transposase and inacti 24.7 5E+02 0.011 23.1 9.1 96 186-324 19-116 (138)
255 PRK12423 LexA repressor; Provi 24.6 1.3E+02 0.0028 27.1 4.5 36 175-210 12-48 (202)
256 PF02724 CDC45: CDC45-like pro 24.5 56 0.0012 34.9 2.6 19 187-205 231-250 (622)
257 PRK15008 HTH-type transcriptio 24.5 1.2E+02 0.0025 26.7 4.1 31 182-212 32-62 (212)
258 cd04763 HTH_MlrA-like Helix-Tu 24.4 68 0.0015 23.6 2.3 21 297-317 3-23 (68)
259 PRK11511 DNA-binding transcrip 24.4 44 0.00095 27.8 1.4 30 288-317 19-48 (127)
260 PRK10668 DNA-binding transcrip 24.4 1.1E+02 0.0025 26.3 4.0 31 181-211 24-54 (215)
261 PRK14165 winged helix-turn-hel 24.2 1.1E+02 0.0023 28.9 4.1 24 188-211 21-44 (217)
262 PF14549 P22_Cro: DNA-binding 24.1 80 0.0017 24.3 2.7 21 190-211 11-31 (60)
263 PRK09954 putative kinase; Prov 23.8 1.3E+02 0.0028 28.7 4.6 33 177-210 7-39 (362)
264 PRK05658 RNA polymerase sigma 23.7 3.5E+02 0.0076 28.7 8.1 43 270-313 553-595 (619)
265 PRK10857 DNA-binding transcrip 23.7 90 0.002 27.8 3.3 31 181-211 18-48 (164)
266 PRK10840 transcriptional regul 23.6 1E+02 0.0023 26.5 3.6 51 272-328 149-199 (216)
267 cd08797 Death_NFkB1_p105 Death 23.1 1.3E+02 0.0028 24.6 3.8 42 176-219 3-45 (76)
268 PRK11303 DNA-binding transcrip 22.8 92 0.002 28.2 3.3 25 189-213 1-25 (328)
269 PF12844 HTH_19: Helix-turn-he 22.7 79 0.0017 22.7 2.3 24 296-319 14-37 (64)
270 COG1414 IclR Transcriptional r 22.4 1.3E+02 0.0029 27.9 4.3 33 178-210 9-41 (246)
271 PRK10820 DNA-binding transcrip 22.2 1.4E+02 0.0029 30.9 4.7 40 171-213 472-511 (520)
272 PF03066 Nucleoplasmin: Nucleo 22.1 30 0.00064 30.7 0.0 8 161-168 138-145 (149)
273 TIGR00498 lexA SOS regulatory 22.1 1.5E+02 0.0032 26.1 4.4 46 274-321 4-53 (199)
274 PF05344 DUF746: Domain of Unk 22.0 49 0.0011 26.5 1.2 33 187-219 12-44 (65)
275 PF08280 HTH_Mga: M protein tr 21.9 1.9E+02 0.0042 21.3 4.3 34 174-209 7-40 (59)
276 TIGR02337 HpaR homoprotocatech 21.8 2.2E+02 0.0048 22.9 5.0 40 169-210 25-64 (118)
277 PF04031 Las1: Las1-like ; In 21.7 98 0.0021 27.5 3.1 23 183-205 96-118 (154)
278 cd04764 HTH_MlrA-like_sg1 Heli 21.5 87 0.0019 22.9 2.4 21 297-317 3-23 (67)
279 PF12840 HTH_20: Helix-turn-he 21.5 2.1E+02 0.0045 20.8 4.3 32 177-209 14-45 (61)
280 PF10668 Phage_terminase: Phag 21.4 1E+02 0.0022 24.1 2.8 25 185-209 19-43 (60)
281 cd02413 40S_S3_KH K homology R 21.2 37 0.00079 27.2 0.3 22 295-316 54-75 (81)
282 PF04297 UPF0122: Putative hel 21.1 80 0.0017 26.9 2.3 24 188-211 33-56 (101)
283 TIGR01481 ccpA catabolite cont 21.1 1E+02 0.0022 27.9 3.2 25 189-213 2-26 (329)
284 PF10446 DUF2457: Protein of u 21.0 89 0.0019 33.0 3.1 8 66-73 20-27 (458)
285 PRK10727 DNA-binding transcrip 20.7 1.1E+02 0.0023 28.3 3.2 25 189-213 2-26 (343)
286 PF01710 HTH_Tnp_IS630: Transp 20.7 89 0.0019 26.0 2.5 21 296-316 20-40 (119)
287 KOG0165 Microtubule-associated 20.6 1.9E+02 0.0042 33.0 5.6 47 87-133 834-888 (1023)
288 PRK14996 TetR family transcrip 20.6 1.2E+02 0.0027 25.7 3.5 33 180-212 20-52 (192)
289 smart00027 EH Eps15 homology d 20.6 2.5E+02 0.0054 22.0 4.9 44 274-317 4-52 (96)
290 PRK13890 conjugal transfer pro 20.6 80 0.0017 26.7 2.3 24 296-319 20-43 (120)
291 PRK00118 putative DNA-binding 20.5 1.2E+02 0.0026 25.7 3.3 44 273-321 17-60 (104)
292 TIGR02985 Sig70_bacteroi1 RNA 20.4 1.1E+02 0.0024 24.5 3.0 44 273-321 113-156 (161)
293 PRK09413 IS2 repressor TnpA; R 20.3 1.4E+02 0.003 24.9 3.6 45 271-320 10-55 (121)
294 PLN03238 probable histone acet 20.3 1.9E+02 0.0041 29.0 5.0 40 171-211 207-246 (290)
295 PRK13890 conjugal transfer pro 20.3 2.2E+02 0.0048 24.0 4.9 34 177-212 9-42 (120)
296 TIGR03879 near_KaiC_dom probab 20.3 1.2E+02 0.0026 24.5 3.1 27 187-213 31-57 (73)
297 PF03374 ANT: Phage antirepres 20.3 1.4E+02 0.0031 23.9 3.6 52 282-336 15-67 (111)
298 PF13551 HTH_29: Winged helix- 20.3 92 0.002 24.0 2.4 31 296-326 14-46 (112)
No 1
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.81 E-value=6.4e-21 Score=161.35 Aligned_cols=68 Identities=21% Similarity=0.358 Sum_probs=61.4
Q ss_pred CCccccccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 260 PVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 260 P~~~~q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
.++...++.+-||+||..||.+||++|.-|||||+++||+||.++.|++.||||||||||||.+--++
T Consensus 10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 34555677899999999999999999999999999999999999999999999999999999765443
No 2
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.76 E-value=4.2e-19 Score=163.95 Aligned_cols=67 Identities=21% Similarity=0.425 Sum_probs=59.3
Q ss_pred CCCCcc-ccccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCC
Q 040593 258 EEPVHD-RQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGV 324 (342)
Q Consensus 258 ~lP~~~-~q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~v 324 (342)
.+|+.. ..++.+-||+||..||++||..|..|+|||+.|||+||.++|||++||||||+|||||++-
T Consensus 27 ~vP~~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~ 94 (228)
T KOG2251|consen 27 GVPYSSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRR 94 (228)
T ss_pred CCCcCccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhH
Confidence 444432 2345679999999999999999999999999999999999999999999999999999864
No 3
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.72 E-value=3.5e-18 Score=162.21 Aligned_cols=63 Identities=25% Similarity=0.388 Sum_probs=59.6
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCCC
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECRK 329 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R~ 329 (342)
..+-||.||.+||+.||+.|.-.||||++.|+-||.+|.|||.|||||||||||||+-.++|-
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 345699999999999999999999999999999999999999999999999999999998873
No 4
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.64 E-value=2.2e-16 Score=112.76 Aligned_cols=55 Identities=24% Similarity=0.501 Sum_probs=52.8
Q ss_pred cccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 269 SAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 269 ~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
..|+.||.+|+.+||.+|..++||+...++.||..+||+..+|++||+|||++++
T Consensus 2 r~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 2 RKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred cCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence 4799999999999999999999999999999999999999999999999999863
No 5
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.58 E-value=3.1e-15 Score=105.42 Aligned_cols=54 Identities=19% Similarity=0.400 Sum_probs=51.7
Q ss_pred ccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 270 AQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 270 kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
.|+.|+..|+..||.+|..++||+...+++||..|||+..+|+.||+|||++.+
T Consensus 3 ~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 3 KRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 578899999999999999999999999999999999999999999999999864
No 6
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.58 E-value=8e-16 Score=142.26 Aligned_cols=58 Identities=22% Similarity=0.298 Sum_probs=56.1
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCC
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGV 324 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~v 324 (342)
..+.||.||.+||.+||+.|..++|.+...|-+||..++|+|++|++||||||+|||-
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk 216 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKK 216 (261)
T ss_pred CCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHH
Confidence 5679999999999999999999999999999999999999999999999999999983
No 7
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.55 E-value=8.9e-15 Score=103.24 Aligned_cols=56 Identities=20% Similarity=0.409 Sum_probs=53.3
Q ss_pred cccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCC
Q 040593 269 SAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGV 324 (342)
Q Consensus 269 ~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~v 324 (342)
..|+.|+..|+..||.+|..++||+...++.||..|||+..+|++||+|||++.+.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 46889999999999999999999999999999999999999999999999998764
No 8
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.53 E-value=2e-15 Score=130.49 Aligned_cols=61 Identities=20% Similarity=0.332 Sum_probs=57.2
Q ss_pred ccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCC
Q 040593 266 HRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPE 326 (342)
Q Consensus 266 ~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~ 326 (342)
.....||.|+..|++.||++|+++||||+.+|+.||..+++++.+|||||||||+||.-..
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 4567999999999999999999999999999999999999999999999999999998443
No 9
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.53 E-value=6.2e-15 Score=140.44 Aligned_cols=58 Identities=17% Similarity=0.284 Sum_probs=55.5
Q ss_pred ccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 266 HRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 266 ~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
+....||.||..||.+||+.|++.+|-++..|-+||+.+||+..+|++||||||+||+
T Consensus 171 K~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWK 228 (309)
T KOG0488|consen 171 KRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWK 228 (309)
T ss_pred ccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHH
Confidence 3455899999999999999999999999999999999999999999999999999997
No 10
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.53 E-value=8.2e-15 Score=110.86 Aligned_cols=52 Identities=6% Similarity=0.168 Sum_probs=49.5
Q ss_pred ccccccCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHhCCChhhHHhhhhhhh
Q 040593 268 WSAQKRLKKVQVKTLEMVYRRSKR----PTDAMISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 268 w~kRTrFT~~QLetLErvF~rT~Y----Pdv~~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
.+.||.||.+|++.||..|++++| ||..+|++||..|||++++|+|||||=+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 368999999999999999999999 9999999999999999999999999953
No 11
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.48 E-value=1.9e-14 Score=130.66 Aligned_cols=58 Identities=16% Similarity=0.274 Sum_probs=55.0
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCC
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGV 324 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~v 324 (342)
..+.||.||.+||..||..|+.++|-....|++||+.++|++.+|+|||||||.|.+-
T Consensus 102 ~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr 159 (197)
T KOG0843|consen 102 PKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKR 159 (197)
T ss_pred CCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHH
Confidence 4578999999999999999999999999999999999999999999999999998653
No 12
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.45 E-value=2.6e-14 Score=138.22 Aligned_cols=62 Identities=24% Similarity=0.420 Sum_probs=58.6
Q ss_pred cccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCC
Q 040593 265 QHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPE 326 (342)
Q Consensus 265 q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~ 326 (342)
++..+.||-||.+||++||..|+++.|||..+||+||--|+|+|.||.|||+||||||+--+
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 46788999999999999999999999999999999999999999999999999999998544
No 13
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.44 E-value=4.6e-14 Score=136.12 Aligned_cols=62 Identities=23% Similarity=0.393 Sum_probs=57.1
Q ss_pred cccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCC
Q 040593 265 QHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPE 326 (342)
Q Consensus 265 q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~ 326 (342)
+...+-||++|+.||+||..+|..++.|...+||+|+..|||..++|||||||||||++--+
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 34567899999999999999999999999999999999999999999999999999986433
No 14
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.42 E-value=7.2e-14 Score=134.12 Aligned_cols=60 Identities=20% Similarity=0.227 Sum_probs=56.5
Q ss_pred ccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 268 WSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 268 w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
.-||.-+||+|+.+||+-|..|.|.+..-|-+|++.|||++++|++||||||+|.|.=.+
T Consensus 236 RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 349999999999999999999999999999999999999999999999999999986553
No 15
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.32 E-value=1.1e-12 Score=115.22 Aligned_cols=62 Identities=23% Similarity=0.371 Sum_probs=56.9
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCC
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECR 328 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R 328 (342)
.-++|++.|.+|+..|+++|..++||+-.+|..|+..+|+|++-||+||||||++.+-..+.
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 45799999999999999999999999999999999999999999999999999987654443
No 16
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.32 E-value=1.1e-12 Score=126.61 Aligned_cols=56 Identities=23% Similarity=0.440 Sum_probs=53.4
Q ss_pred ccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 268 WSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 268 w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
.+.||+|+..|+.+||+.|.+++||++..|++||+.|+||+.+|||||+|||+++.
T Consensus 177 rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~r 232 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWR 232 (354)
T ss_pred cccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhh
Confidence 45799999999999999999999999999999999999999999999999999864
No 17
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.28 E-value=1.2e-12 Score=127.19 Aligned_cols=68 Identities=16% Similarity=0.265 Sum_probs=60.2
Q ss_pred CCCCCccccccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCC
Q 040593 257 VEEPVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGV 324 (342)
Q Consensus 257 ~~lP~~~~q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~v 324 (342)
+-++.....|-.+-||.||.+||..||+.|-+..|-+.-.|=+||..+||||..|+|||||||+|++-
T Consensus 171 g~~a~sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKR 238 (408)
T KOG0844|consen 171 GPYANSADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKR 238 (408)
T ss_pred CccccCccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhh
Confidence 33443344556678999999999999999999999999999999999999999999999999999873
No 18
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.25 E-value=3.9e-12 Score=121.68 Aligned_cols=59 Identities=19% Similarity=0.300 Sum_probs=55.3
Q ss_pred ccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCC
Q 040593 268 WSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPE 326 (342)
Q Consensus 268 w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~ 326 (342)
.+-||.||.+||+.|...|+-++|.+-.-|++||+.++|.|++|++||||+|||-+-..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 35799999999999999999999999999999999999999999999999999977544
No 19
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.23 E-value=4.1e-12 Score=118.14 Aligned_cols=57 Identities=18% Similarity=0.302 Sum_probs=53.9
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
+.--||-||.+||..||+.|+..+|.+++.|-+++..++|++-+|++||||||||.+
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaK 200 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAK 200 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHH
Confidence 445799999999999999999999999999999999999999999999999999864
No 20
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.21 E-value=1.1e-11 Score=112.82 Aligned_cols=59 Identities=24% Similarity=0.370 Sum_probs=56.6
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCC
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVP 325 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp 325 (342)
.+.++.+||.+|+..||+.|.-.+|-.-.-+..||+.+||..++|.||||||||+|+-+
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 47899999999999999999999999999999999999999999999999999999865
No 21
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.18 E-value=9.6e-12 Score=116.46 Aligned_cols=56 Identities=16% Similarity=0.290 Sum_probs=54.0
Q ss_pred ccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 268 WSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 268 w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
..-||.|+..|+-.||..|...+|.+.+.|..||+.+.|+|-+|++||||||.||+
T Consensus 105 KktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwK 160 (268)
T KOG0485|consen 105 KKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWK 160 (268)
T ss_pred ccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHH
Confidence 35799999999999999999999999999999999999999999999999999997
No 22
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.18 E-value=1.2e-11 Score=118.99 Aligned_cols=60 Identities=15% Similarity=0.318 Sum_probs=55.8
Q ss_pred ccccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 264 RQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 264 ~q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
+++....|--||+.|+-+||+-|...+|.+...||.||..|+|++-+|++||||||.|-|
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~K 209 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTK 209 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhh
Confidence 556667888999999999999999999999999999999999999999999999998854
No 23
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.11 E-value=2.1e-11 Score=116.59 Aligned_cols=53 Identities=25% Similarity=0.333 Sum_probs=50.6
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 271 QKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 271 RTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
|-.+|.+|..+||+.|.-++|.+|.-..+||..++|+|++|++||||||||++
T Consensus 203 RvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKER 255 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKER 255 (317)
T ss_pred eEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHH
Confidence 44689999999999999999999999999999999999999999999999986
No 24
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.10 E-value=5.9e-11 Score=111.17 Aligned_cols=56 Identities=11% Similarity=0.272 Sum_probs=53.4
Q ss_pred ccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 268 WSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 268 w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
+--||.|+..||+.|.+-|++|+|.-.-.|-+||..|||+--+|++||||||.|.+
T Consensus 123 RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~K 178 (245)
T KOG0850|consen 123 RKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFK 178 (245)
T ss_pred cCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHH
Confidence 44799999999999999999999999999999999999999999999999999864
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.03 E-value=1.1e-10 Score=109.73 Aligned_cols=58 Identities=19% Similarity=0.315 Sum_probs=54.8
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCC
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGV 324 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~v 324 (342)
.-+.|-+|+.+||..||+.|..++||-...|-+||..+|+++++|.|||||||.||+-
T Consensus 167 rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRK 224 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRK 224 (288)
T ss_pred ccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhh
Confidence 3457889999999999999999999999999999999999999999999999999974
No 26
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=98.97 E-value=1.6e-10 Score=104.67 Aligned_cols=58 Identities=17% Similarity=0.358 Sum_probs=54.7
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCC
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGV 324 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~v 324 (342)
..-.||.|+..||..||+-|++.+|.+-..|.+||-.++|++.+|+.||||||+|.+-
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk 157 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKK 157 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 3458999999999999999999999999999999999999999999999999999764
No 27
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=98.90 E-value=7.2e-10 Score=109.82 Aligned_cols=63 Identities=17% Similarity=0.287 Sum_probs=58.5
Q ss_pred ccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCC
Q 040593 266 HRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECR 328 (342)
Q Consensus 266 ~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R 328 (342)
+...|||.|.......||+.|.+++.|+...+..||..++|...+|.|||+|||.|.|-.+..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~~ 355 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITPF 355 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCCC
Confidence 446799999999999999999999999999999999999999999999999999998866553
No 28
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.62 E-value=2.3e-08 Score=86.69 Aligned_cols=139 Identities=17% Similarity=0.169 Sum_probs=94.3
Q ss_pred hhchHHHHHHHHHHHhcCc--cccHHHHHHHhcCCHHHHHHHhcCCCC--chh---hhcccCCCCCCCcccccccCCCcc
Q 040593 169 RLKNWQLRKLAYALKTGRR--KVSVKSLAAELCLDRAVVLEMLGDPPP--NLL---MLSATLPDKPTPTVLVNEVKHSEP 241 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRR--KvsIk~LA~EL~LDRa~VL~wLR~ppP--~ll---~mSa~lpdE~~~~~~~~E~~~~~~ 241 (342)
....||+..|.+|...=-- -..-..||..+.|+-..|..|+.|.=- +.. ..+.......... .+..
T Consensus 66 ~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~------~~~~- 138 (235)
T KOG0490|consen 66 KFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGT------APPS- 138 (235)
T ss_pred CCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCC------CCcc-
Confidence 5667999999998765300 012347899999999999999887431 111 1111101000000 0000
Q ss_pred cccccccccCCCCCCCCCCCccccccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 242 IVAETTVHAVEPKSKVEEPVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 242 v~~ets~~a~e~~~~~~lP~~~~q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
.......+.....+....||.|+..|+++++..|..++||+...+++|+..+|+++..|||||||+|++
T Consensus 139 -----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~ 207 (235)
T KOG0490|consen 139 -----------ASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAK 207 (235)
T ss_pred -----------ccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHH
Confidence 011111122333445678999999999999999999999999999999999999999999999999999
Q ss_pred cCCC
Q 040593 322 EGVP 325 (342)
Q Consensus 322 d~vp 325 (342)
.+-.
T Consensus 208 ~~~~ 211 (235)
T KOG0490|consen 208 LRKH 211 (235)
T ss_pred HHhh
Confidence 8644
No 29
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.04 E-value=3.6e-06 Score=59.48 Aligned_cols=34 Identities=24% Similarity=0.517 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 288 RSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 288 rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
.++||+...+++||+.|||+..+|..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4799999999999999999999999999999963
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.01 E-value=5.5e-06 Score=80.04 Aligned_cols=57 Identities=18% Similarity=0.383 Sum_probs=52.1
Q ss_pred ccc---ccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 267 RWS---AQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 267 ~w~---kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
-|. .--.|+..---.|...|..++||+.....+||+.|||+--+|-.||+|||.+++
T Consensus 173 IWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 173 IWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred cccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 465 334688888999999999999999999999999999999999999999999987
No 31
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.83 E-value=2.1e-05 Score=81.35 Aligned_cols=52 Identities=25% Similarity=0.495 Sum_probs=50.3
Q ss_pred ccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 270 AQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 270 kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
-|..||..|..||..+|..++||+..|.+.|++.+||..+.|+.||-|-|.+
T Consensus 423 PRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 423 PRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred ceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 3999999999999999999999999999999999999999999999998876
No 32
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=97.68 E-value=1e-05 Score=79.31 Aligned_cols=58 Identities=17% Similarity=0.394 Sum_probs=54.7
Q ss_pred ccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 266 HRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 266 ~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
...+|||.+-.-.-..||.+|...++|+..-+-.||.++.|-.-+|.|||.|.|.|-+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQK 365 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQK 365 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHH
Confidence 3468999999999999999999999999999999999999999999999999999865
No 33
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.20 E-value=0.00026 Score=79.16 Aligned_cols=59 Identities=24% Similarity=0.439 Sum_probs=55.1
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCC
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVP 325 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp 325 (342)
....||.|+..||.+|...|..-.||.....|-|-..++|+.++|+|||||-|+|.+-+
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~ 961 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA 961 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence 44599999999999999999999999999999999999999999999999999987543
No 34
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=97.18 E-value=0.00027 Score=68.73 Aligned_cols=58 Identities=14% Similarity=0.327 Sum_probs=53.3
Q ss_pred ccccccccCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 266 HRWSAQKRLKKVQVKTLEMVYR---RSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 266 ~~w~kRTrFT~~QLetLErvF~---rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
+..++|..|++.-.+.|...|- .++||+....++||+..|++-++|-.||.|+|.+.+
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIryk 247 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYK 247 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehh
Confidence 3468999999999999999995 689999999999999999999999999999997653
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.12 E-value=0.0052 Score=47.21 Aligned_cols=44 Identities=16% Similarity=0.462 Sum_probs=32.6
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 278 QVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 278 QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
.++.|+++|...+++.-....+|..++||+-.+|+.||--|+.+
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 45779999999999999999999999999999999999988654
No 36
>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=95.84 E-value=0.019 Score=43.15 Aligned_cols=41 Identities=29% Similarity=0.404 Sum_probs=37.7
Q ss_pred chHHHHHHHHHHHhc----CccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 171 KNWQLRKLAYALKTG----RRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 171 ~~WQl~rLarAL~~G----RRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
-.-|.+.|..|+..| -|++++++||++||+.++.|.+-||.
T Consensus 2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 2 TDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 356999999999999 79999999999999999999999885
No 37
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=95.82 E-value=0.014 Score=63.32 Aligned_cols=63 Identities=30% Similarity=0.455 Sum_probs=53.3
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCCCccccCC
Q 040593 271 QKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECRKPFQRSD 335 (342)
Q Consensus 271 RTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R~~~qrs~ 335 (342)
-+.|+.- +..|...|..+..|.......||+.+|||-+.|++||+|++++ .+...|.|-|-+-
T Consensus 561 ~k~~~~p-~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~-e~sv~rsps~psg 623 (1007)
T KOG3623|consen 561 SKQFNHP-TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAE-EMSVERSPSQPSG 623 (1007)
T ss_pred ccccCCc-HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhh-hhhhccCccCCCC
Confidence 3455555 8999999999999999999999999999999999999999998 5666666664433
No 38
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=95.20 E-value=0.03 Score=50.15 Aligned_cols=43 Identities=40% Similarity=0.511 Sum_probs=41.2
Q ss_pred hhchHHHHHHHHHHHhc----CccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 169 RLKNWQLRKLAYALKTG----RRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~G----RRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.|-.+|++.|..|++.| -|++++++||++||+-...+.+-||.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRr 201 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRR 201 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 79999999999999999 69999999999999999999999985
No 39
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=95.05 E-value=0.028 Score=39.72 Aligned_cols=44 Identities=20% Similarity=0.352 Sum_probs=33.8
Q ss_pred hhhhhchHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 166 REVRLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 166 r~~~L~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
||-.+...|.+.+-.-++.| .+|.+||+++|+.|+.|.-+|+.+
T Consensus 2 Rp~~~~~~~~~~i~~l~~~G---~si~~IA~~~gvsr~TvyR~l~~~ 45 (45)
T PF02796_consen 2 RPPKLSKEQIEEIKELYAEG---MSIAEIAKQFGVSRSTVYRYLNKN 45 (45)
T ss_dssp SSSSSSHCCHHHHHHHHHTT-----HHHHHHHTTS-HHHHHHHHCC-
T ss_pred cCCCCCHHHHHHHHHHHHCC---CCHHHHHHHHCcCHHHHHHHHhcC
Confidence 45566666777788888899 899999999999999999999864
No 40
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=94.91 E-value=0.014 Score=55.38 Aligned_cols=61 Identities=26% Similarity=0.416 Sum_probs=51.9
Q ss_pred cccccccccCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCC
Q 040593 265 QHRWSAQKRLKKVQVKTLEMVYRR---SKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVP 325 (342)
Q Consensus 265 q~~w~kRTrFT~~QLetLErvF~r---T~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp 325 (342)
+..|+.+..|.+.....|+.-... .+||+......||..|||+..+|-.||-|.|-+..=|
T Consensus 237 ~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 237 QSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 457999999999999999854333 3799999999999999999999999999998775533
No 41
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=93.35 E-value=0.26 Score=52.52 Aligned_cols=15 Identities=47% Similarity=0.820 Sum_probs=11.7
Q ss_pred HHHHHHHHHHhCCcc
Q 040593 120 DKLATELAEALGDVD 134 (342)
Q Consensus 120 a~~e~el~~a~gd~~ 134 (342)
..|...|++|||.-+
T Consensus 702 ~~~~~~l~~aL~~~~ 716 (784)
T PF04931_consen 702 EEFRSALAKALGDAD 716 (784)
T ss_pred HHHHHHHHHHhcccc
Confidence 468888999998654
No 42
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=90.57 E-value=0.43 Score=33.97 Aligned_cols=43 Identities=23% Similarity=0.208 Sum_probs=37.4
Q ss_pred hhchHHHHHHHHHHHhcCcc--ccHHHHHHHhcCCHHHHHHHhcC
Q 040593 169 RLKNWQLRKLAYALKTGRRK--VSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRRK--vsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.+..+|+..|...+..+..= .-+..||.+|||+...|-.|+.|
T Consensus 6 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 6 RFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp SSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHH
Confidence 56789999999999997653 34789999999999999999875
No 43
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=90.00 E-value=0.47 Score=33.25 Aligned_cols=42 Identities=21% Similarity=0.202 Sum_probs=36.9
Q ss_pred hchHHHHHHHHHHHhcCc--cccHHHHHHHhcCCHHHHHHHhcC
Q 040593 170 LKNWQLRKLAYALKTGRR--KVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 170 L~~WQl~rLarAL~~GRR--KvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+..=|+..|..++..+.. +..|..||++|||+...|-.|+.|
T Consensus 7 ~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~n 50 (56)
T smart00389 7 FTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQN 50 (56)
T ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHH
Confidence 556689999999999985 556899999999999999999986
No 44
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=89.89 E-value=0.29 Score=52.13 Aligned_cols=11 Identities=18% Similarity=0.498 Sum_probs=7.0
Q ss_pred cHHHHHHHHHH
Q 040593 87 DPFEALFSLLE 97 (342)
Q Consensus 87 da~E~LF~~LE 97 (342)
.+|+.|+..|+
T Consensus 623 ~~l~~ll~vl~ 633 (784)
T PF04931_consen 623 SGLQLLLDVLD 633 (784)
T ss_pred HHHHHHHHHhc
Confidence 45566666776
No 45
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=89.52 E-value=0.33 Score=37.25 Aligned_cols=44 Identities=14% Similarity=0.124 Sum_probs=37.1
Q ss_pred hhchHHHHHHHHHHHhcCc------cccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 169 RLKNWQLRKLAYALKTGRR------KVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRR------KvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
.+.+.|+.+|......-.. .--+..||.+|||++.+|-=|+-|+
T Consensus 7 ~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~ 56 (58)
T TIGR01565 7 KFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNN 56 (58)
T ss_pred CCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccC
Confidence 5678999999988876654 3368899999999999999999886
No 46
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=87.95 E-value=0.16 Score=56.69 Aligned_cols=12 Identities=25% Similarity=0.783 Sum_probs=4.7
Q ss_pred CCCCCCCCCCHH
Q 040593 106 TIDDDDEEIDEE 117 (342)
Q Consensus 106 s~~dddd~isee 117 (342)
|++|++||-|.|
T Consensus 1447 s~eDn~de~sde 1458 (1516)
T KOG1832|consen 1447 SSEDNEDEVSDE 1458 (1516)
T ss_pred ccccccccccCc
Confidence 334444444433
No 47
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=87.87 E-value=1.6 Score=25.51 Aligned_cols=31 Identities=26% Similarity=0.372 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHh
Q 040593 176 RKLAYALKTGRRKVSVKSLAAELCLDRAVVLEML 209 (342)
Q Consensus 176 ~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wL 209 (342)
..+...+..|. +++.+|+++|+-+..|-.|+
T Consensus 12 ~~i~~~~~~~~---s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 12 EEARRLLAAGE---SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred HHHHHHHHcCC---CHHHHHHHHCCCHHHHHHhC
Confidence 34444555554 99999999999999998875
No 48
>PF13518 HTH_28: Helix-turn-helix domain
Probab=86.61 E-value=1.2 Score=30.78 Aligned_cols=30 Identities=23% Similarity=0.310 Sum_probs=24.8
Q ss_pred HHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 180 YALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 180 rAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
.++..|- |++.+|+++|+++..|-.|++..
T Consensus 7 ~~~~~g~---s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 7 ELYLEGE---SVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred HHHHcCC---CHHHHHHHHCCCHhHHHHHHHHH
Confidence 3444553 99999999999999999999763
No 49
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=86.35 E-value=1.5 Score=32.32 Aligned_cols=46 Identities=11% Similarity=0.109 Sum_probs=33.2
Q ss_pred cccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhh
Q 040593 269 SAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 269 ~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
.+|+.||-.|=-.+=..|.... ....||+..|++.+.|..|.+||.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 4788899887655555566665 688999999999999999999974
No 50
>PF13551 HTH_29: Winged helix-turn helix
Probab=85.98 E-value=4.3 Score=31.43 Aligned_cols=95 Identities=16% Similarity=0.177 Sum_probs=58.4
Q ss_pred HHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhcccCCCCCCCcccccccCCCcccccccccccCCCCCCCCC
Q 040593 180 YALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEE 259 (342)
Q Consensus 180 rAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~lpdE~~~~~~~~E~~~~~~v~~ets~~a~e~~~~~~l 259 (342)
..++.|.= +|+.+|+.||+.|..|-.|++..--.= ++.. +
T Consensus 6 ~l~~~g~~--~~~~ia~~lg~s~~Tv~r~~~~~~~~G--~~~l------------------------------------~ 45 (112)
T PF13551_consen 6 LLLAEGVS--TIAEIARRLGISRRTVYRWLKRYREGG--IEGL------------------------------------L 45 (112)
T ss_pred HHHHcCCC--cHHHHHHHHCcCHHHHHHHHHHHHccc--HHHH------------------------------------H
Confidence 44555543 699999999999999999998743111 0000 0
Q ss_pred CCccccccccccccCCHHHHHHHHHHhhhcCCCC--HHHHHHHHHH-------hCCChhhHHhhhh
Q 040593 260 PVHDRQHRWSAQKRLKKVQVKTLEMVYRRSKRPT--DAMISSIVQV-------TNLPRRRIVKWFE 316 (342)
Q Consensus 260 P~~~~q~~w~kRTrFT~~QLetLErvF~rT~YPd--v~~RE~LA~~-------t~LpesrVQVWFQ 316 (342)
+.. ....+.++.++.+|.+.|...+...+.-+ .-....|+.. +.++.+.|..|++
T Consensus 46 ~~~--~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 46 PRK--PRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred hcc--ccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 100 01122333489999999999999766321 1223333332 3678888888875
No 51
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=84.37 E-value=1.8 Score=30.25 Aligned_cols=43 Identities=23% Similarity=0.218 Sum_probs=36.9
Q ss_pred hhchHHHHHHHHHHHhcCc--cccHHHHHHHhcCCHHHHHHHhcC
Q 040593 169 RLKNWQLRKLAYALKTGRR--KVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRR--KvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.+...|+..|+..+..... ..-|..||++|||....|-.|++|
T Consensus 6 ~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 6 RFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQN 50 (59)
T ss_pred cCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 5677899999999999764 234889999999999999999986
No 52
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=82.75 E-value=2.1 Score=31.70 Aligned_cols=35 Identities=20% Similarity=0.227 Sum_probs=28.5
Q ss_pred HHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 175 LRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 175 l~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
++.+..++..| .+|..||+++|+..+.+-.|++..
T Consensus 13 ~~~v~~~~~~g---~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 13 LQAVREYLESG---ESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp HHHHHHHHHHH---CHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHCC---CceEeeecccccccccccHHHHHH
Confidence 45566666666 799999999999999999999875
No 53
>COG5414 TATA-binding protein-associated factor [Transcription]
Probab=80.87 E-value=2.9 Score=42.09 Aligned_cols=105 Identities=26% Similarity=0.348 Sum_probs=57.5
Q ss_pred hcCCCCCC-CCCCCCCCHHHHHHHHHHHHHHhCCcccccc-------CCCCCCCCCCCcccC---CCCCCchhHhhhhhh
Q 040593 100 LKNDDSTI-DDDDEEIDEEDLDKLATELAEALGDVDMDMS-------DTATDGTESDNNEAH---KEDGEDEEEEEEREV 168 (342)
Q Consensus 100 Lknd~~s~-~dddd~iseed~a~~e~el~~a~gd~~~~~~-------~~~~~~~~~~~d~~~---~~~~~~~~~~~er~~ 168 (342)
||.++-++ .|..|+.+||||...+-|...-.++.+.-.. .-+..+++.++++++ +-..+++-++.+|-.
T Consensus 257 l~ke~Q~~e~e~~eGM~eeDLd~gaae~~~~e~se~~kEq~~E~~~~~e~~~~E~~~d~~de~~Ee~E~dde~~En~r~~ 336 (392)
T COG5414 257 LKKEKQGAEEEGEEGMSEEDLDVGAAEIENKEVSEGDKEQQQEEVENAEAHKEEVQSDRPDEIGEEKEEDDENEENERHT 336 (392)
T ss_pred cchhhhcchhhhccccchhhhhhhHHHHhhhhccccchhhhhchhhhhhhhcccccccCccchhhhcccCchhhHHHHHH
Confidence 34444444 3334788899997777666666654321110 111111111111111 222233335556666
Q ss_pred hhchHHHHHHHHHHHhcCccc--------------cHHHHHHHhcCCHHH
Q 040593 169 RLKNWQLRKLAYALKTGRRKV--------------SVKSLAAELCLDRAV 204 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRRKv--------------sIk~LA~EL~LDRa~ 204 (342)
.|-.=-+.-|+..+..-||+. +|+.|-+||.|-|.-
T Consensus 337 ~Ll~d~lnELE~~i~~~r~~~~~AtNPiL~~RF~~~~n~l~kElElkrkq 386 (392)
T COG5414 337 ELLADELNELEKGIEEKRRQMESATNPILQKRFESQLNVLLKELELKRKQ 386 (392)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 676666777888888878775 478888999888753
No 54
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=80.45 E-value=2.1 Score=31.53 Aligned_cols=40 Identities=23% Similarity=0.297 Sum_probs=30.6
Q ss_pred hhchHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 169 RLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.|--+|--.+-+.+..|- +..+||+++|+.++.|-.|+++
T Consensus 6 ~LTl~eK~~iI~~~e~g~---s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 6 SLTLEEKLEIIKRLEEGE---SKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp S--HHHHHHHHHHHHCTT----HHHHHHHHT--CCHHHHHHHC
T ss_pred cCCHHHHHHHHHHHHcCC---CHHHHHHHhCCCHHHHHHHHHh
Confidence 455566667778899998 8999999999999999999987
No 55
>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=79.45 E-value=2.4 Score=30.23 Aligned_cols=33 Identities=21% Similarity=0.299 Sum_probs=26.6
Q ss_pred HHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 178 LAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 178 LarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
+-.+++......++++||+.+|++|+.|-.+|.
T Consensus 8 iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345667777778999999999999999988775
No 56
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=78.19 E-value=2.4 Score=30.03 Aligned_cols=36 Identities=22% Similarity=0.294 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 173 WQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 173 WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
-|...++.-++.| .|+..||+.||..++.|-.+||.
T Consensus 8 ~eR~~I~~l~~~G---~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 8 EERNQIEALLEQG---MSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ----HHHHHHCS------HHHHHHHTT--HHHHHHHHHH
T ss_pred hHHHHHHHHHHcC---CCHHHHHHHHCcCcHHHHHHHhc
Confidence 3444566667766 89999999999999999988863
No 57
>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=76.14 E-value=2.1 Score=30.94 Aligned_cols=23 Identities=30% Similarity=0.356 Sum_probs=20.1
Q ss_pred cccHHHHHHHhcCCHHHHHHHhc
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR 210 (342)
+++|.+||++||++-..||..|.
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l~ 25 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKLF 25 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH-
T ss_pred ceEHHHHHHHHCcCHHHHHHHHH
Confidence 67899999999999999999993
No 58
>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=74.72 E-value=7.3 Score=27.50 Aligned_cols=33 Identities=21% Similarity=0.300 Sum_probs=23.1
Q ss_pred HHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 178 LAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 178 LarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
+-..|......++++.||.+||+.|..|-.-++
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 334453334449999999999999999976554
No 59
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=73.77 E-value=5.2 Score=26.10 Aligned_cols=45 Identities=7% Similarity=0.191 Sum_probs=34.9
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
..++..|...++..|. ......++|..+|++...|..|.+.-+.+
T Consensus 9 ~~l~~~~~~~~~~~~~-----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 9 DKLPEREREVILLRFG-----EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred HhCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 3577888888888774 22356778999999999999999876654
No 60
>PRK13558 bacterio-opsin activator; Provisional
Probab=73.56 E-value=5.3 Score=40.51 Aligned_cols=43 Identities=28% Similarity=0.359 Sum_probs=40.9
Q ss_pred hhchHHHHHHHHHHHhcC----ccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 169 RLKNWQLRKLAYALKTGR----RKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GR----RKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.|-.=|.+.|..|+..|= |.++..+||++||+.++.|-+-||.
T Consensus 607 ~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~ 653 (665)
T PRK13558 607 DLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRA 653 (665)
T ss_pred hCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 689999999999999996 9999999999999999999999985
No 61
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=72.92 E-value=14 Score=34.80 Aligned_cols=123 Identities=15% Similarity=0.130 Sum_probs=69.9
Q ss_pred HHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhcccCCCCCCCcccccccCCCcccccccccccCCC
Q 040593 174 QLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVEP 253 (342)
Q Consensus 174 Ql~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~lpdE~~~~~~~~E~~~~~~v~~ets~~a~e~ 253 (342)
+++++...|. +.+..++..||++||++-..|.+++..-.....-|...+.++.... ....+.+...
T Consensus 138 ~~~~~~~~l~-~~~~~t~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~-----~~l~~~l~d~-------- 203 (284)
T PRK06596 138 NLRKAKKRLG-WLNPEEVEMVAEELGVSEEEVREMESRLSGQDASLDAPIDDDDEES-----GAPQDYLEDK-------- 203 (284)
T ss_pred HHHHHHHHhc-cCCCCCHHHHHHHhCcCHHHHHHHHHHhcCCCcCcCCCCCCCCCCc-----chHHHHcCCC--------
Confidence 4566667775 3467779999999999999999987543333222222222110000 0000111110
Q ss_pred CCCCCCCCcc-cc-------cc--ccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhh
Q 040593 254 KSKVEEPVHD-RQ-------HR--WSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFE 316 (342)
Q Consensus 254 ~~~~~lP~~~-~q-------~~--w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQ 316 (342)
...|... .. .. ...=..++..|-..|...|.. + .....++||..+|++..+|..+=.
T Consensus 204 ---~~~p~~~~~~~~~~~~~~~~L~~al~~L~~rEr~VL~lry~~--~-~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 204 ---SSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEARWLD--D-DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred ---CCCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC--C-CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 0011110 00 00 112346888899999998843 1 345578999999999999987643
No 62
>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=72.60 E-value=4.5 Score=30.53 Aligned_cols=27 Identities=33% Similarity=0.404 Sum_probs=20.5
Q ss_pred hcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 184 TGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 184 ~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
+-++.+|+..||.+|+++.+.|-++|.
T Consensus 10 ~~~~~~S~~eLa~~~~~s~~~ve~mL~ 36 (69)
T PF09012_consen 10 RERGRVSLAELAREFGISPEAVEAMLE 36 (69)
T ss_dssp HHS-SEEHHHHHHHTT--HHHHHHHHH
T ss_pred HHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 346789999999999999999987763
No 63
>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=71.53 E-value=9.6 Score=26.41 Aligned_cols=35 Identities=31% Similarity=0.392 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 174 QLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 174 Ql~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
|.+.| .+|...-+ ++++.||+.+|+.++.|-..|+
T Consensus 5 ~~~Il-~~l~~~~~-~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 5 QRKIL-NYLRENPR-ITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp HHHHH-HHHHHCTT-S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHH-HHHHHcCC-CCHHHHHHHhCCCHHHHHHHHH
Confidence 34445 44444333 9999999999999999987765
No 64
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=71.43 E-value=1.5 Score=48.65 Aligned_cols=9 Identities=44% Similarity=0.653 Sum_probs=3.6
Q ss_pred CCCCHHHHH
Q 040593 112 EEIDEEDLD 120 (342)
Q Consensus 112 d~iseed~a 120 (342)
|++.++|+.
T Consensus 881 deddd~d~~ 889 (988)
T KOG2038|consen 881 DEDDDEDEN 889 (988)
T ss_pred ccccccchh
Confidence 343444443
No 65
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=71.02 E-value=4.7 Score=27.94 Aligned_cols=25 Identities=20% Similarity=0.280 Sum_probs=19.3
Q ss_pred cccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
-.|++.+|+.||+.|..|-.|++..
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 5799999999999999999999874
No 66
>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=70.75 E-value=5.1 Score=26.66 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=21.9
Q ss_pred ccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 189 VSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
.+++++|+-||+.|..|..|+++.
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcC
Confidence 478999999999999999999874
No 67
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=70.46 E-value=15 Score=32.81 Aligned_cols=111 Identities=11% Similarity=0.171 Sum_probs=61.2
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhcccCCCCCCCcccccccCCCcccccccccccCCCCCCCCCCCccccc
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEEPVHDRQH 266 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~lpdE~~~~~~~~E~~~~~~v~~ets~~a~e~~~~~~lP~~~~q~ 266 (342)
|..++.+||++||++...|...+....+ ..-|...+.++...... ..+.+... ..... . +-....
T Consensus 112 r~pt~~ela~~l~~~~~~v~~~~~~~~~-~~sl~~~~~~~~~~~~~-----~~d~~~~~------~~~~~-~--~~~~~~ 176 (231)
T TIGR02885 112 REPTINELAEALGVSPEEIVMALESARS-PQSLYDTVHQDDGDPIY-----LLDQIADK------GSEDS-D--WLEKIA 176 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHccC-CcCcccCCCCCCCCcch-----hhhhcCCC------CccHH-h--HHHHHH
Confidence 4456999999999999999988765332 11111211111100000 00010000 00000 0 000011
Q ss_pred cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhh
Q 040593 267 RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 267 ~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQN 317 (342)
-...-..|+..+.+.+...|.. .....+||..+|++..+|..+-+.
T Consensus 177 l~~~l~~L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~ 222 (231)
T TIGR02885 177 LKEAISKLDERERQIIMLRYFK-----DKTQTEVANMLGISQVQVSRLEKK 222 (231)
T ss_pred HHHHHHcCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 1123458889999999888742 346899999999999999887543
No 68
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=70.05 E-value=14 Score=21.27 Aligned_cols=40 Identities=10% Similarity=0.256 Sum_probs=29.4
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhh
Q 040593 271 QKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWF 315 (342)
Q Consensus 271 RTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWF 315 (342)
++.|+..+...+-..|.. .+ ...++|..+|++...|..|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 445677777767666653 33 56788999999999998884
No 69
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=69.66 E-value=12 Score=24.98 Aligned_cols=48 Identities=10% Similarity=0.151 Sum_probs=37.6
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCC
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPE 326 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~ 326 (342)
.|+..|...+...+.. ....+||+.+|+++..|..|.+.-+.+-++..
T Consensus 3 ~l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~~~~~kl~~~~ 50 (58)
T smart00421 3 SLTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLSNIMRKLGVRS 50 (58)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
Confidence 4788888888764422 25588999999999999999998777777654
No 70
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=67.67 E-value=26 Score=33.27 Aligned_cols=128 Identities=13% Similarity=0.121 Sum_probs=70.5
Q ss_pred HHHHHHHHHHHh-----cCccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhcccCCCCCCCcccccccCCCcccccccc
Q 040593 173 WQLRKLAYALKT-----GRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETT 247 (342)
Q Consensus 173 WQl~rLarAL~~-----GRRKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~lpdE~~~~~~~~E~~~~~~v~~ets 247 (342)
++++++..++.. || .-++.+||+.||++...|.++...-.++.+-|...+.++..... ..++.+..+
T Consensus 129 ~~~~~~~~~~~~~~~~l~~-~pt~~eiA~~l~~~~~~v~~~~~~~~~~~~SLd~~~~~~~~~~~-----~l~d~i~d~-- 200 (289)
T PRK07500 129 FNLRRLRARLAQADEELTK-QEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRS-----ERMDFLVDD-- 200 (289)
T ss_pred HHHHHHHHHHHhhhcccCC-CCCHHHHHHHhCcCHHHHHHHHHHhcCCCccccCCCCCCCCCcc-----cHHHhccCC--
Confidence 345566666655 44 34699999999999999987653322232222222211111000 001111100
Q ss_pred cccCCCCCCCCCCCcccc--------c--cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhh
Q 040593 248 VHAVEPKSKVEEPVHDRQ--------H--RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 248 ~~a~e~~~~~~lP~~~~q--------~--~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQN 317 (342)
...|-.... . -...=..|+..|-+.|...|- |=.....++||..+|+++.+|..+-..
T Consensus 201 ---------~~~pe~~~~~~~~~~~~~~~l~~al~~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~ 268 (289)
T PRK07500 201 ---------SPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEAR 268 (289)
T ss_pred ---------CCCchHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 001111100 0 011225789999999999884 223446799999999999999988765
Q ss_pred hhh
Q 040593 318 KRA 320 (342)
Q Consensus 318 RRA 320 (342)
-+.
T Consensus 269 Al~ 271 (289)
T PRK07500 269 ALE 271 (289)
T ss_pred HHH
Confidence 443
No 71
>cd00131 PAX Paired Box domain
Probab=67.55 E-value=74 Score=27.10 Aligned_cols=36 Identities=11% Similarity=0.210 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 174 QLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 174 Ql~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
...++-.+++.| .+...+|+.||+.+..|.-|++..
T Consensus 22 ~R~rIv~~~~~G---~s~~~iA~~~~Vs~~tV~r~i~r~ 57 (128)
T cd00131 22 IRQRIVELAQSG---IRPCDISRQLRVSHGCVSKILNRY 57 (128)
T ss_pred HHHHHHHHHHcC---CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 445556777777 689999999999999999999753
No 72
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=67.53 E-value=6.5 Score=28.24 Aligned_cols=27 Identities=22% Similarity=0.373 Sum_probs=21.4
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
.|++++++||+..|+.++.|=.|+++.
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 477899999999999999999999997
No 73
>PRK10403 transcriptional regulator NarP; Provisional
Probab=67.39 E-value=7.8 Score=31.48 Aligned_cols=49 Identities=12% Similarity=0.102 Sum_probs=42.3
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
.||..+.+.|+..... ..+.+||+.++++++.|.+..+|=|.|-++..+
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~ 201 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR 201 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCH
Confidence 5899999999877654 456889999999999999999999999998764
No 74
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=67.11 E-value=14 Score=23.34 Aligned_cols=26 Identities=15% Similarity=0.286 Sum_probs=24.0
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
++++.+.||+.+|+..+.|-.|+.+.
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 57899999999999999999999885
No 75
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=67.03 E-value=8.1 Score=31.56 Aligned_cols=50 Identities=14% Similarity=0.113 Sum_probs=43.5
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
..||+.+.+.|+-..+. ..+++||+.++++++.|.+..++=|.|-+|.++
T Consensus 136 ~~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~~~~ 185 (196)
T PRK10360 136 DPLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLGVSND 185 (196)
T ss_pred cCCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence 46999999999887754 368899999999999999999999999998764
No 76
>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=66.46 E-value=16 Score=25.88 Aligned_cols=40 Identities=18% Similarity=0.223 Sum_probs=31.7
Q ss_pred chHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 171 KNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 171 ~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
..=|...|..-...|...+++.+||+.|+++++.|-..++
T Consensus 4 t~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~ 43 (62)
T PF12802_consen 4 TPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVK 43 (62)
T ss_dssp THHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3446667777777777789999999999999999987765
No 77
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=66.00 E-value=15 Score=26.13 Aligned_cols=39 Identities=13% Similarity=0.243 Sum_probs=29.7
Q ss_pred chHHHHHHHHHHHhcCccccHHHHHHHhcC-CHHHHHHHhcC
Q 040593 171 KNWQLRKLAYALKTGRRKVSVKSLAAELCL-DRAVVLEMLGD 211 (342)
Q Consensus 171 ~~WQl~rLarAL~~GRRKvsIk~LA~EL~L-DRa~VL~wLR~ 211 (342)
....+.+....|..+ +.+|++||.++|+ +..-.-..+|.
T Consensus 35 ~~~r~~~a~~~l~~~--~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 35 RDRRLERARRLLRDT--DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHHHHHHHcC--CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 344556666666666 8999999999999 99887776653
No 78
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=65.53 E-value=12 Score=28.35 Aligned_cols=34 Identities=21% Similarity=0.283 Sum_probs=27.0
Q ss_pred HHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 178 LAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 178 LarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+-..|......+++.+||+++|++++.|-..|+.
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~ 43 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNT 43 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHH
Confidence 3445666656899999999999999999777754
No 79
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=65.46 E-value=12 Score=26.05 Aligned_cols=34 Identities=15% Similarity=0.257 Sum_probs=28.4
Q ss_pred HHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 178 LAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 178 LarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+......|=++++|.+||+++|+.++.+-..+.+
T Consensus 6 ~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~ 39 (47)
T PF00440_consen 6 LELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPS 39 (47)
T ss_dssp HHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSS
T ss_pred HHHHHHhCHHhCCHHHHHHHHccchhhHHHHcCC
Confidence 4455688999999999999999999988766554
No 80
>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=65.35 E-value=16 Score=29.67 Aligned_cols=37 Identities=16% Similarity=0.179 Sum_probs=28.8
Q ss_pred HHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCCC
Q 040593 175 LRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPP 214 (342)
Q Consensus 175 l~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ppP 214 (342)
...++ .|.. .+++|++||+.+|+.++.|=--|.++++
T Consensus 9 ~~I~e-~l~~--~~~ti~dvA~~~gvS~~TVsr~L~~~~~ 45 (80)
T TIGR02844 9 LEIGK-YIVE--TKATVRETAKVFGVSKSTVHKDVTERLP 45 (80)
T ss_pred HHHHH-HHHH--CCCCHHHHHHHhCCCHHHHHHHhcCCCC
Confidence 33344 4444 6789999999999999999999977644
No 81
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=64.27 E-value=12 Score=29.51 Aligned_cols=35 Identities=26% Similarity=0.347 Sum_probs=27.3
Q ss_pred HHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 176 RKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 176 ~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+++-++|..+.| ++++.||+.||+++..|...++.
T Consensus 6 ~~il~~L~~~~~-~~~~~la~~l~~s~~tv~~~l~~ 40 (108)
T smart00344 6 RKILEELQKDAR-ISLAELAKKVGLSPSTVHNRVKR 40 (108)
T ss_pred HHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHHH
Confidence 455566766543 88999999999999999776654
No 82
>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=64.21 E-value=11 Score=28.49 Aligned_cols=42 Identities=12% Similarity=0.242 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHhCCChhhHHhhh
Q 040593 274 LKKVQVKTLEMVYRRSKR--PTDAMISSIVQVTNLPRRRIVKWF 315 (342)
Q Consensus 274 FT~~QLetLErvF~rT~Y--Pdv~~RE~LA~~t~LpesrVQVWF 315 (342)
||..|.++|..+|..-=| |-....+.||..+|++.+.+..-.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 689999999999998754 888999999999999998876543
No 83
>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=64.16 E-value=9.7 Score=31.16 Aligned_cols=43 Identities=33% Similarity=0.313 Sum_probs=33.9
Q ss_pred hhchHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 169 RLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
+...|=++-|-|.|+.|+ -|++..||+.||.+-..|-.-|..-
T Consensus 20 ~~~~~L~r~LLr~LA~G~-PVt~~~LA~a~g~~~e~v~~~L~~~ 62 (77)
T PF12324_consen 20 GGFAWLLRPLLRLLAKGQ-PVTVEQLAAALGWPVEEVRAALAAM 62 (77)
T ss_dssp TTHHHHHHHHHHHHTTTS--B-HHHHHHHHT--HHHHHHHHHH-
T ss_pred CccHHHHHHHHHHHHcCC-CcCHHHHHHHHCCCHHHHHHHHHhC
Confidence 567899999999999985 7999999999999999998887653
No 84
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=63.55 E-value=17 Score=27.64 Aligned_cols=34 Identities=26% Similarity=0.257 Sum_probs=25.9
Q ss_pred HHHHHHHh-cCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 177 KLAYALKT-GRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 177 rLarAL~~-GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
++-.+|+. |-..++.++||++|||++..|-..|.
T Consensus 10 ~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 10 KILEFLENSGDETSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 34444444 44359999999999999999988775
No 85
>COG5593 Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]
Probab=63.14 E-value=8.9 Score=41.59 Aligned_cols=26 Identities=19% Similarity=0.389 Sum_probs=13.2
Q ss_pred CCCCCCCCc-HHHHHHH---HHHHhhcCCC
Q 040593 79 IKDSDEEDD-PFEALFS---LLEEDLKNDD 104 (342)
Q Consensus 79 ~~~~~~d~d-a~E~LF~---~LEeDLknd~ 104 (342)
+.+||-||+ -.-||-+ ++|+|-...+
T Consensus 680 d~d~emde~eiw~alv~srp~~e~d~ddse 709 (821)
T COG5593 680 DSDDEMDENEIWSALVKSRPDVEDDSDDSE 709 (821)
T ss_pred CccccccHHHHHHHHhccCCccccCccccc
Confidence 344454554 4556654 5666544433
No 86
>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=62.58 E-value=8.7 Score=25.22 Aligned_cols=22 Identities=14% Similarity=0.157 Sum_probs=20.7
Q ss_pred cHHHHHHHhcCCHHHHHHHhcC
Q 040593 190 SVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 190 sIk~LA~EL~LDRa~VL~wLR~ 211 (342)
++.++|+.||+.+..|..|.++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 6889999999999999999986
No 87
>PRK05572 sporulation sigma factor SigF; Validated
Probab=62.02 E-value=31 Score=31.54 Aligned_cols=43 Identities=12% Similarity=0.165 Sum_probs=34.5
Q ss_pred ccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhh
Q 040593 270 AQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 270 kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQN 317 (342)
.-..|+..|.+.|...|. ......+||..+|++...|..|-..
T Consensus 199 ~l~~L~~~~~~v~~l~~~-----~~~s~~eIA~~lgis~~~V~~~~~r 241 (252)
T PRK05572 199 AIRELDERERLIVYLRYF-----KDKTQSEVAKRLGISQVQVSRLEKK 241 (252)
T ss_pred HHHcCCHHHHHHHHHHHh-----CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345789999999998884 2356689999999999999887554
No 88
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=60.92 E-value=15 Score=24.79 Aligned_cols=47 Identities=11% Similarity=0.203 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCC
Q 040593 274 LKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPE 326 (342)
Q Consensus 274 FT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~ 326 (342)
|+..|.+.+.-.+. .....++|..+|++...|..|...-+.+-+++.
T Consensus 1 l~~~e~~i~~~~~~------~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~~ 47 (57)
T cd06170 1 LTPREREVLRLLAE------GKTNKEIADILGISEKTVKTHLRNIMRKLGVKS 47 (57)
T ss_pred CCHHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCC
Confidence 35566777765432 235688999999999999999987677666653
No 89
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=60.55 E-value=18 Score=27.44 Aligned_cols=35 Identities=26% Similarity=0.218 Sum_probs=27.4
Q ss_pred HHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 177 KLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 177 rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
..|+.|=- .-.+|++||.+||+.+..|-.|.+-..
T Consensus 4 ~~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r~~ 38 (58)
T PF06056_consen 4 EQARSLYL--QGWSIKEIAEELGVPRSTVYSWKDRYK 38 (58)
T ss_pred HHHHHHHH--cCCCHHHHHHHHCCChHHHHHHHHhhC
Confidence 44555543 467999999999999999999987643
No 90
>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=60.02 E-value=20 Score=25.50 Aligned_cols=32 Identities=28% Similarity=0.299 Sum_probs=21.9
Q ss_pred HHHHHHHhcCccccHHHHHHHhcCCHHHHHHHh
Q 040593 177 KLAYALKTGRRKVSVKSLAAELCLDRAVVLEML 209 (342)
Q Consensus 177 rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wL 209 (342)
+|-.+|..+ =+.|...||++|||..+.|..=+
T Consensus 7 ~Il~~Lq~d-~r~s~~~la~~lglS~~~v~~Ri 38 (42)
T PF13404_consen 7 KILRLLQED-GRRSYAELAEELGLSESTVRRRI 38 (42)
T ss_dssp HHHHHHHH--TTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHc-CCccHHHHHHHHCcCHHHHHHHH
Confidence 444555555 44799999999999999998644
No 91
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=60.01 E-value=18 Score=25.38 Aligned_cols=41 Identities=10% Similarity=0.230 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhh
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDK 318 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNR 318 (342)
.|+..|-+.|...| | ....-+++|..+|+++..|..+...-
T Consensus 4 ~L~~~er~vi~~~y----~-~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRY----F-EGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHH----T-ST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh----c-CCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 57889999999999 2 23447889999999999999887643
No 92
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=59.98 E-value=10 Score=27.41 Aligned_cols=50 Identities=10% Similarity=0.128 Sum_probs=40.8
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
..||..+++.|.-..+- ....++|..+|++.+.|..+..+=+.|.|++.+
T Consensus 2 ~~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~~ 51 (58)
T PF00196_consen 2 PSLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLGVKNR 51 (58)
T ss_dssp GSS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SSH
T ss_pred CccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhCCCCH
Confidence 36899999999887764 346788999999999999999999999998864
No 93
>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=59.95 E-value=22 Score=26.80 Aligned_cols=27 Identities=30% Similarity=0.315 Sum_probs=24.0
Q ss_pred cCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 185 GRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 185 GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
++..+++++||+.|++.++.|-++|+.
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~ 45 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKR 45 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHH
Confidence 788999999999999999999998863
No 94
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=59.79 E-value=30 Score=30.68 Aligned_cols=43 Identities=12% Similarity=0.173 Sum_probs=34.9
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhh
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
..|+..|-+.|...|-. .....+||..+|++...|..|...=+
T Consensus 177 ~~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~ 219 (227)
T TIGR02980 177 AALPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRAL 219 (227)
T ss_pred HcCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 57889999999888742 34678999999999999999976443
No 95
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=59.31 E-value=50 Score=30.73 Aligned_cols=126 Identities=17% Similarity=0.183 Sum_probs=69.1
Q ss_pred HHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhcccCC--CCCCCcccccccCCCcccccccccccCC
Q 040593 175 LRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLP--DKPTPTVLVNEVKHSEPIVAETTVHAVE 252 (342)
Q Consensus 175 l~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~lp--dE~~~~~~~~E~~~~~~v~~ets~~a~e 252 (342)
++++.+.+..++..+++..||+.||++...|.+.+...... .+|---| ++..... ...+.+..+ .
T Consensus 126 ~~~~~~~~~~~~~~~~~~eiA~~l~~~~~~v~~~~~~~~~~--~~Sld~~~~~~~~~~~-----~~~~~l~d~-----~- 192 (270)
T TIGR02392 126 LRKMKKRLQGWLNPEEVEAIAEELGVSEREVREMESRLSGQ--DMSLNASIDDDEDDGG-----APIAYLVDK-----T- 192 (270)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHhCCCHHHHHHHHHHccCC--CccCCCCCCCCCCccc-----cHHHHhcCC-----C-
Confidence 34455555434666569999999999999999875432221 2332212 1111000 000000000 0
Q ss_pred CCCCCCCCCccc-cccc---------cccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 253 PKSKVEEPVHDR-QHRW---------SAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 253 ~~~~~~lP~~~~-q~~w---------~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
+ -|-... ...| ..=..|+..|-..|...|-. +. ...-.+||..+|++..+|..+..+-..|
T Consensus 193 ~-----~pe~~~~~~~~~~~~~~~L~~al~~L~~rer~vl~l~y~~--~~-~~t~~eIA~~lgvS~~~V~q~~~~Al~k 263 (270)
T TIGR02392 193 S-----DPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLD--DD-KLTLQELAAEYGVSAERIRQIEKNAMKK 263 (270)
T ss_pred C-----ChHHHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHhcC--CC-CcCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 0 011100 0001 12246888899999998842 22 3346899999999999999887654433
No 96
>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=59.25 E-value=14 Score=25.22 Aligned_cols=28 Identities=7% Similarity=-0.015 Sum_probs=24.9
Q ss_pred cCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 185 GRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 185 GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
.++..+.++||..+|+.++.|-.|.++.
T Consensus 12 ~~~gltq~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 12 KALGLTQADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 4568889999999999999999999873
No 97
>COG1427 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=58.67 E-value=7 Score=37.87 Aligned_cols=50 Identities=18% Similarity=0.303 Sum_probs=42.6
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCC
Q 040593 275 KKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVP 325 (342)
Q Consensus 275 T~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp 325 (342)
...|...+|...++..|+ ..+.+++++.+|||++.++-.|.|-|-..+-.
T Consensus 180 ~~~~~~~~~~~~~~~~~~-~ei~~~~a~~lglp~~~~~eYy~~~~Y~l~~e 229 (252)
T COG1427 180 PFYKRALLEFEETKAKFP-AEILKEAAKRLGLPRSDVEEYYTNIRYSLGTE 229 (252)
T ss_pred CchhhhHHHHHHHHHhhh-HHHHHHHHHHcCCCHHHHHHHHHHheeecCHH
Confidence 456777788888899999 99999999999999999999999977665543
No 98
>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=58.60 E-value=24 Score=24.34 Aligned_cols=37 Identities=32% Similarity=0.381 Sum_probs=28.1
Q ss_pred hHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 172 NWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 172 ~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.||...|.... .+. +++++||+.||+++..|-.+|+.
T Consensus 7 ~~~~~il~~l~-~~~--~~~~ei~~~~~i~~~~i~~~l~~ 43 (78)
T cd00090 7 PTRLRILRLLL-EGP--LTVSELAERLGLSQSTVSRHLKK 43 (78)
T ss_pred hHHHHHHHHHH-HCC--cCHHHHHHHHCcCHhHHHHHHHH
Confidence 46777776544 444 99999999999999988666543
No 99
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=58.03 E-value=26 Score=23.35 Aligned_cols=24 Identities=33% Similarity=0.340 Sum_probs=21.3
Q ss_pred cccHHHHHHHhcCCHHHHHHHhcC
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.+++.+||+.|++.++.|-..|+.
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 599999999999999999877754
No 100
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=57.92 E-value=20 Score=27.64 Aligned_cols=39 Identities=23% Similarity=0.233 Sum_probs=31.1
Q ss_pred hhchHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 169 RLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
.|..+|...+...+-.| .++++||++||+.++.|-.+++
T Consensus 110 ~L~~~~~~ii~~~~~~g---~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG---LSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred hCCHHHHHHHhhHHhcC---CCHHHHHHHHCCCHHHHHHHHH
Confidence 46677777776665555 5999999999999999988775
No 101
>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=57.71 E-value=22 Score=26.28 Aligned_cols=40 Identities=25% Similarity=0.347 Sum_probs=29.8
Q ss_pred hchHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 170 LKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 170 L~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
|..=+.+.+..-++.| ..++++||+.||++|..|-..|+.
T Consensus 6 Ls~~E~~vy~~Ll~~~--~~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 6 LSENEAKVYLALLKNG--PATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp HHHHHHHHHHHHHHHC--HEEHHHHHHHHTSSHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4444555555555554 589999999999999999887763
No 102
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=57.15 E-value=28 Score=26.07 Aligned_cols=28 Identities=29% Similarity=0.372 Sum_probs=21.5
Q ss_pred HhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 183 KTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 183 ~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+-|| ..++..||+.||++...|-.++..
T Consensus 16 ~lgr-~Pt~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 16 ELGR-EPTDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHSS---BHHHHHHHHTS-HHHHHHHHHH
T ss_pred HhCC-CCCHHHHHHHHcccHHHHHHHHHh
Confidence 3455 799999999999999999988875
No 103
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=57.07 E-value=25 Score=22.29 Aligned_cols=27 Identities=15% Similarity=0.297 Sum_probs=24.3
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
+.+.+...+|+.+|+.+..|-.|+.+.
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence 357899999999999999999999974
No 104
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=56.94 E-value=3.6 Score=35.31 Aligned_cols=7 Identities=57% Similarity=0.696 Sum_probs=0.0
Q ss_pred hHhhhhh
Q 040593 161 EEEEERE 167 (342)
Q Consensus 161 ~~~~er~ 167 (342)
+++++-|
T Consensus 36 ee~de~p 42 (101)
T PF09026_consen 36 EEEDEVP 42 (101)
T ss_dssp -------
T ss_pred ccccccc
Confidence 3344444
No 105
>KOG1446 consensus Histone H3 (Lys4) methyltransferase complex and RNA cleavage factor II complex, subunit SWD2 [RNA processing and modification; Chromatin structure and dynamics; Posttranslational modification, protein turnover, chaperones]
Probab=56.88 E-value=3.9 Score=40.80 Aligned_cols=35 Identities=40% Similarity=0.705 Sum_probs=23.5
Q ss_pred ccccccc--chhhhccC--ccchhcccCCCCCCCCcCCC
Q 040593 7 TSICTST--SRAVHRLS--PSQYLRLFPGHHRKPTNLLL 41 (342)
Q Consensus 7 ~~~~~~~--~~~~~~~~--~~~~~~~~~~~~~~p~~l~l 41 (342)
+.||.|| .-.++-|| --+|||.||||+.+=..|..
T Consensus 70 ~~i~sStk~d~tIryLsl~dNkylRYF~GH~~~V~sL~~ 108 (311)
T KOG1446|consen 70 TVIHSSTKEDDTIRYLSLHDNKYLRYFPGHKKRVNSLSV 108 (311)
T ss_pred eEEEccCCCCCceEEEEeecCceEEEcCCCCceEEEEEe
Confidence 4456665 34555554 56899999999987655444
No 106
>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=56.42 E-value=27 Score=24.69 Aligned_cols=35 Identities=26% Similarity=0.429 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 174 QLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 174 Ql~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
|...|..-...|- ++++.||..++++++.|-.+++
T Consensus 5 q~~iL~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~ 39 (59)
T PF01047_consen 5 QFRILRILYENGG--ITQSELAEKLGISRSTVTRIIK 39 (59)
T ss_dssp HHHHHHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHcCC--CCHHHHHHHHCCChhHHHHHHH
Confidence 5666777777777 9999999999999999887765
No 107
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=56.39 E-value=14 Score=33.71 Aligned_cols=29 Identities=14% Similarity=0.193 Sum_probs=25.9
Q ss_pred cCccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 185 GRRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 185 GRRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
++.|++|++||+++|+.++.|=--|.+.+
T Consensus 3 ~~~~~Ti~dIA~~agVS~~TVSr~Ln~~~ 31 (342)
T PRK10014 3 TAKKITIHDVALAAGVSVSTVSLVLSGKG 31 (342)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHCCCC
Confidence 46689999999999999999999998755
No 108
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 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 groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=56.11 E-value=17 Score=26.51 Aligned_cols=24 Identities=29% Similarity=0.589 Sum_probs=22.2
Q ss_pred cHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 190 SVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 190 sIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
+|++||+++|+..+.|=-.|.+++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~ 24 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPP 24 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCS
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCC
Confidence 589999999999999999999885
No 109
>PF12728 HTH_17: Helix-turn-helix domain
Probab=55.84 E-value=13 Score=25.96 Aligned_cols=24 Identities=25% Similarity=0.328 Sum_probs=21.8
Q ss_pred ccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 189 VSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
.+++++|.-||+.++.|..|++..
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC
Confidence 478999999999999999999873
No 110
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=55.48 E-value=18 Score=30.04 Aligned_cols=35 Identities=9% Similarity=0.115 Sum_probs=27.8
Q ss_pred HHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 175 LRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 175 l~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
++.+...+..| .+|..||+++|+..+.|-.|++..
T Consensus 19 ~~aV~~~~~~g---~sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 19 IAIVQQSFEPG---MTVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred HHHHHHHHcCC---CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34445555554 599999999999999999999875
No 111
>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=55.32 E-value=17 Score=33.11 Aligned_cols=32 Identities=22% Similarity=0.254 Sum_probs=27.0
Q ss_pred HHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 180 YALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 180 rAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.++...++..++++||++|||.|+.|.-+|..
T Consensus 16 ~~l~~~~~~~~l~eia~~lglpksT~~RlL~t 47 (248)
T TIGR02431 16 EAFGAERPRLTLTDVAEATGLTRAAARRFLLT 47 (248)
T ss_pred HHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44566778899999999999999999887754
No 112
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=55.27 E-value=4.1 Score=47.17 Aligned_cols=65 Identities=15% Similarity=0.055 Sum_probs=56.3
Q ss_pred cccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCCC
Q 040593 265 QHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECRK 329 (342)
Q Consensus 265 q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R~ 329 (342)
......||+++..|+..|-..|....||--.++..+++.+++-.+.+.+||++++.++|-+-.|.
T Consensus 442 ~e~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~ 506 (1406)
T KOG1146|consen 442 AEPLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRL 506 (1406)
T ss_pred hhhhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccccccc
Confidence 33445899999999999999999999999999999999999999998888888777777665554
No 113
>PHA01976 helix-turn-helix protein
Probab=55.11 E-value=26 Score=25.41 Aligned_cols=27 Identities=15% Similarity=0.247 Sum_probs=24.5
Q ss_pred cCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 185 GRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 185 GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
-.+..+.++||+.+|+.++.|-.|.+.
T Consensus 12 ~~~glt~~~lA~~~gvs~~~v~~~e~g 38 (67)
T PHA01976 12 NARAWSAPELSRRAGVRHSLIYDFEAD 38 (67)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 346789999999999999999999987
No 114
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=54.88 E-value=13 Score=33.59 Aligned_cols=26 Identities=27% Similarity=0.322 Sum_probs=23.7
Q ss_pred cccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
|.||..||.-.||+|..|-.=|++-+
T Consensus 1 ~~nI~qlA~~~g~~R~TV~~RL~~~~ 26 (152)
T PF07278_consen 1 KWNINQLAEAFGLHRQTVAKRLKGAN 26 (152)
T ss_pred CCCHHHHHHHHcccHHHHHHHHccCC
Confidence 68999999999999999999999843
No 115
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=54.43 E-value=49 Score=32.60 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=33.7
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhh
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFE 316 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQ 316 (342)
..|+..+-..|...|.-..+ ....-++||+.+||++.||...-.
T Consensus 304 ~~L~~rEr~Vl~lrygl~~~-~~~tl~EIa~~lgvs~erVrQi~~ 347 (367)
T PRK09210 304 DTLTDREENVLRLRFGLDDG-RTRTLEEVGKVFGVTRERIRQIEA 347 (367)
T ss_pred HhCCHHHHHHHHHHhccCCC-CCccHHHHHHHHCCCHHHHHHHHH
Confidence 46888899999998864321 123468999999999999998843
No 116
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=54.28 E-value=13 Score=33.82 Aligned_cols=28 Identities=14% Similarity=0.389 Sum_probs=25.4
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
|++++|++||+.+|+.++.|=--|.+.+
T Consensus 3 ~~~~ti~dIA~~agVS~~TVSrvLn~~~ 30 (331)
T PRK14987 3 KKRPVLQDVADRVGVTKMTVSRFLRNPE 30 (331)
T ss_pred CCCCcHHHHHHHhCCCHHHhhhhhCCCC
Confidence 6679999999999999999999997765
No 117
>KOG2038 consensus CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis; Transcription]
Probab=53.83 E-value=12 Score=41.85 Aligned_cols=6 Identities=50% Similarity=0.950 Sum_probs=2.3
Q ss_pred HHHhCC
Q 040593 127 AEALGD 132 (342)
Q Consensus 127 ~~a~gd 132 (342)
.|-+||
T Consensus 903 dEdi~~ 908 (988)
T KOG2038|consen 903 DEDIGD 908 (988)
T ss_pred chhccc
Confidence 333443
No 118
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=53.40 E-value=9.5 Score=27.38 Aligned_cols=25 Identities=12% Similarity=0.272 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCChhhHHhhhhhhhh
Q 040593 296 MISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 296 ~RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
....||+.+|+++..|..|+.++..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~ 36 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPS 36 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT--
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccc
Confidence 5678999999999999999998843
No 119
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=52.98 E-value=34 Score=32.00 Aligned_cols=45 Identities=9% Similarity=0.155 Sum_probs=35.3
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
..|+..|...|...|.. .....+||..+|++..+|..|...-+.+
T Consensus 214 ~~L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~k 258 (264)
T PRK07122 214 AALPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLAR 258 (264)
T ss_pred HcCCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46888888899988842 3446899999999999999987654443
No 120
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=52.79 E-value=23 Score=29.26 Aligned_cols=34 Identities=26% Similarity=0.308 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 176 RKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 176 ~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+.|..--+.|| +|++.||++|||.+..|..-++.
T Consensus 12 ~IL~~L~~d~r--~~~~eia~~lglS~~~v~~Ri~~ 45 (154)
T COG1522 12 RILRLLQEDAR--ISNAELAERVGLSPSTVLRRIKR 45 (154)
T ss_pred HHHHHHHHhCC--CCHHHHHHHHCCCHHHHHHHHHH
Confidence 34444444555 99999999999999999987764
No 121
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=52.77 E-value=34 Score=23.78 Aligned_cols=26 Identities=23% Similarity=0.363 Sum_probs=22.1
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.+..+.++||+.+|+.++.|=.|+++
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 45678899999999999999999999
No 122
>PRK11569 transcriptional repressor IclR; Provisional
Probab=51.95 E-value=20 Score=33.35 Aligned_cols=32 Identities=16% Similarity=0.156 Sum_probs=26.1
Q ss_pred HHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 179 AYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 179 arAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
-.+++...+-+++++||+.|||+++.|.-+|.
T Consensus 34 L~~l~~~~~~~~lseia~~lglpksTv~RlL~ 65 (274)
T PRK11569 34 LEWIAESNGSVALTELAQQAGLPNSTTHRLLT 65 (274)
T ss_pred HHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 34456677889999999999999999976653
No 123
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=51.91 E-value=27 Score=27.98 Aligned_cols=49 Identities=8% Similarity=0.051 Sum_probs=40.9
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
.||..+.+.|.-. . ..| ...++|+.++++++.|..|.+|=|.|-+|..+
T Consensus 149 ~lt~~e~~vl~l~-~-~g~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~~~ 197 (211)
T PRK15369 149 LLTPRERQILKLI-T-EGY----TNRDIAEQLSISIKTVETHRLNMMRKLDVHKV 197 (211)
T ss_pred CCCHHHHHHHHHH-H-CCC----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence 4899999999874 3 223 36789999999999999999999999998764
No 124
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=51.81 E-value=40 Score=22.44 Aligned_cols=27 Identities=26% Similarity=0.396 Sum_probs=22.9
Q ss_pred HHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 182 LKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 182 L~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+..| .+++.+|..||+.++.|-.+++.
T Consensus 15 ~~~g---~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 15 LAEG---LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred HHcC---CCHHHHHHHHCCCHHHHHHHHHH
Confidence 4556 59999999999999999988763
No 125
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=50.96 E-value=22 Score=29.01 Aligned_cols=51 Identities=12% Similarity=0.068 Sum_probs=43.0
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCC
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECR 328 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R 328 (342)
-.+|..+...|....+. ..+++||+.++++.+.|.++-++=|.|-+|..+.
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~~~~ 198 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLGLHSIV 198 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHH
Confidence 34889999999865444 6688999999999999999999999999987653
No 126
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=50.81 E-value=52 Score=33.20 Aligned_cols=128 Identities=14% Similarity=0.176 Sum_probs=75.5
Q ss_pred HHHHHHHHHhc-CccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhcccCC--CCCCCcccccccCCCcccccccccccC
Q 040593 175 LRKLAYALKTG-RRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLP--DKPTPTVLVNEVKHSEPIVAETTVHAV 251 (342)
Q Consensus 175 l~rLarAL~~G-RRKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~lp--dE~~~~~~~~E~~~~~~v~~ets~~a~ 251 (342)
++|..+.|..+ -|...+..||.+||+..+.|..+++-... .+|--.| ++..+ ..++-.....
T Consensus 191 l~r~~r~l~q~~~r~p~~eeia~~l~~~~~~V~~m~~~~~~---~~SLd~~ig~ded~-------~l~d~leD~~----- 255 (342)
T COG0568 191 LRRVKRELLQELGREPTPEEIAEELGVSPDKVREMLKRASE---PISLDTPIGDDEDS-------ELGDFLEDDK----- 255 (342)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHhccc---CcccCCcCCCCccc-------HHHHHhhcCC-----
Confidence 34455555554 46778899999999999999998875433 2222111 11100 1111100000
Q ss_pred CCCCCCCCCC-ccccccc-----c-ccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC
Q 040593 252 EPKSKVEEPV-HDRQHRW-----S-AQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG 323 (342)
Q Consensus 252 e~~~~~~lP~-~~~q~~w-----~-kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~ 323 (342)
...|. ++.+..| . -.+.+|..+...|..-|... .-...+-++|+..+|+++.||..+=.+-=.|-+
T Consensus 256 -----~~~p~~~~~~~~~~~~~~~~L~~~Lt~rE~~Vi~~R~gl~-~~~~~TLeevg~~~~isrERvRQIE~kAl~KLr 328 (342)
T COG0568 256 -----SVSPEDAVERESLKEDLNEVLAEALTERERRVIRLRFGLD-DGEPKTLEELGEEFGISRERVRQIEAKALRKLR 328 (342)
T ss_pred -----cCCHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHhccC-CCCcchHHHHHHHhCCcHHHHHHHHHHHHHHHH
Confidence 00010 1111111 1 11229999999999999987 333678899999999999999988665444433
No 127
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=50.78 E-value=13 Score=27.40 Aligned_cols=46 Identities=11% Similarity=0.185 Sum_probs=30.6
Q ss_pred ccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhh
Q 040593 270 AQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 270 kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
+|++||.++-..+=..+ .-....+.++|..+||+.+.|..|-+.-+
T Consensus 3 ~r~~ys~e~K~~~v~~~----~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREY----LESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHH----HHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHH----HHCCCceEeeecccccccccccHHHHHHh
Confidence 57888887755544444 22357789999999999999999987766
No 128
>PRK09492 treR trehalose repressor; Provisional
Probab=50.74 E-value=17 Score=32.62 Aligned_cols=28 Identities=18% Similarity=0.338 Sum_probs=24.8
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
+.|++|++||+.+|+.++.|=--|.+.+
T Consensus 2 ~~~~ti~dIA~~agVS~~TVSrvLn~~~ 29 (315)
T PRK09492 2 QNKLTIKDIARLSGVGKSTVSRVLNNES 29 (315)
T ss_pred CCCCcHHHHHHHhCCCHHHHhHHhCCCC
Confidence 3578999999999999999999998754
No 129
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=50.62 E-value=12 Score=26.89 Aligned_cols=25 Identities=24% Similarity=0.466 Sum_probs=20.8
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
|=++++.+|+-+|+.|+.+-.|.++
T Consensus 2 rll~~~ev~~~~g~s~~ti~~~~k~ 26 (51)
T PF05930_consen 2 RLLRIKEVAELLGVSRSTIYRLIKD 26 (51)
T ss_dssp -EE-HHHHHHHHSS-HHHHHHHHHH
T ss_pred ccccHHHHHHHHCCCHHHHHHHHhc
Confidence 5578999999999999999999997
No 130
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=50.48 E-value=24 Score=33.18 Aligned_cols=7 Identities=14% Similarity=0.344 Sum_probs=3.0
Q ss_pred ccCCHHH
Q 040593 272 KRLKKVQ 278 (342)
Q Consensus 272 TrFT~~Q 278 (342)
..||.++
T Consensus 183 ~~lTQeE 189 (240)
T PF05764_consen 183 RPLTQEE 189 (240)
T ss_pred CCCCHHH
Confidence 3444444
No 131
>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=50.18 E-value=36 Score=24.46 Aligned_cols=33 Identities=24% Similarity=0.404 Sum_probs=24.4
Q ss_pred HHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCCC
Q 040593 180 YALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPP 214 (342)
Q Consensus 180 rAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ppP 214 (342)
.+++.|. .||...|+..|++|..+-..++.-.|
T Consensus 10 ~~v~~g~--~S~r~AA~~ygVp~sTL~~r~~g~~~ 42 (45)
T PF05225_consen 10 EAVKNGK--MSIRKAAKKYGVPRSTLRRRLRGKPS 42 (45)
T ss_dssp HHHHTTS--S-HHHHHHHHT--HHHHHHHHHHTTT
T ss_pred HHHHhCC--CCHHHHHHHHCcCHHHHHHHHcCCCC
Confidence 4455666 99999999999999999988887554
No 132
>PHA00542 putative Cro-like protein
Probab=50.17 E-value=37 Score=26.72 Aligned_cols=26 Identities=8% Similarity=0.084 Sum_probs=23.7
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
+..++..||+.||+.++.|-.|+++.
T Consensus 30 ~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 30 AGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 46899999999999999999999874
No 133
>PF05044 HPD: Homeo-prospero domain; InterPro: IPR007738 The homeobox gene Prox1 is expressed in a subpopulation of endothelial cells that, after budding from veins, gives rise to the mammalian lymphatic system []. Prox1 has been found to be an early specific marker for the developing liver and pancreas in the mammalian foregut endoderm []. This family contains an atypical homeobox domain.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2LMD_A 1XPX_A 1MIJ_A.
Probab=50.16 E-value=9.9 Score=34.81 Aligned_cols=48 Identities=19% Similarity=0.483 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCC---hhhHHhhhhhhhh
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLP---RRRIVKWFEDKRA 320 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~Lp---esrVQVWFQNRRA 320 (342)
.||+.+|..-.-.|--|+||+..+...----+... -+++..||.|=|.
T Consensus 2 ~Ltp~HLkKaKlMFfytRYPss~~LK~yFpDv~Fnr~~TsQLiKWFSNFRE 52 (158)
T PF05044_consen 2 GLTPMHLKKAKLMFFYTRYPSSNMLKSYFPDVKFNRCNTSQLIKWFSNFRE 52 (158)
T ss_dssp SS-HHHHHHHHHHCTT-SS-HHHHHHHCTTTS---HHHHHHHHHHHHHHHH
T ss_pred CCChHHHhhhhheeeeecCCchHHHHHhCchhhhhhhhHHHHHHHhccchh
Confidence 58899999999999999999999876543322222 4788999999874
No 134
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=49.95 E-value=7.9 Score=31.12 Aligned_cols=39 Identities=8% Similarity=0.083 Sum_probs=32.6
Q ss_pred HHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhh
Q 040593 282 LEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 282 LErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
.+.+|...+|-......+||..+|+|+..|.+|+.+...
T Consensus 20 ~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 20 AEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 456777777778888999999999999999999986443
No 135
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=49.29 E-value=76 Score=30.86 Aligned_cols=116 Identities=16% Similarity=0.103 Sum_probs=66.5
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhcccCCCCCCCcccccccCCCcccccccccccCCCCCCCCCCCccccc
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEEPVHDRQH 266 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~lpdE~~~~~~~~E~~~~~~v~~ets~~a~e~~~~~~lP~~~~q~ 266 (342)
|..++..||..||+.-..|...+..+.+ ..-+-+.+.+++..+ -.+.+..+ . ...|-...+.
T Consensus 188 r~~t~~eiA~~l~~~~~~v~~~l~~~~~-~~sld~~~~~~~~~~-------l~d~l~d~-------~---~~~pe~~~~~ 249 (325)
T PRK05657 188 HEPSAEEIAELLDKPVDDVSRMLALNER-ITSLDTPLGGDPEKS-------LLDILADE-------Q---ENGPEDTTQD 249 (325)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHhccC-CcccCCCCCCCCCcc-------hhhhccCC-------C---CCCHHHHHHH
Confidence 5667999999999999999888875443 111111111111100 00000000 0 0001000000
Q ss_pred ------cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 267 ------RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 267 ------~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
-...=..|+..|...|...|.-.. -.....++||..+|++..+|.++...-+.+
T Consensus 250 ~e~~~~L~~aL~~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~k 309 (325)
T PRK05657 250 DDMKQSIVKWLFELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRR 309 (325)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 011224789999999999884433 345667999999999999999997655443
No 136
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=49.21 E-value=69 Score=29.38 Aligned_cols=42 Identities=7% Similarity=0.162 Sum_probs=34.2
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhh
Q 040593 271 QKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 271 RTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQN 317 (342)
-..|+..+.+.|+..|.. .....+||..+|++..+|..+-.+
T Consensus 207 l~~L~~~er~vi~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~ 248 (258)
T PRK08215 207 MKKLNDREKLILNLRFFQ-----GKTQMEVAEEIGISQAQVSRLEKA 248 (258)
T ss_pred HHcCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 357999999999999842 345789999999999999887654
No 137
>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=49.02 E-value=28 Score=30.56 Aligned_cols=41 Identities=20% Similarity=0.150 Sum_probs=29.6
Q ss_pred hchHHHHHHHHHH---HhcCccccHHHHHHHhcCC-HHHHHHHhc
Q 040593 170 LKNWQLRKLAYAL---KTGRRKVSVKSLAAELCLD-RAVVLEMLG 210 (342)
Q Consensus 170 L~~WQl~rLarAL---~~GRRKvsIk~LA~EL~LD-Ra~VL~wLR 210 (342)
|..=|.+.|.... ..+-...++++||+.||++ ++.|-..|+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~ 48 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLK 48 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHH
Confidence 3344555555544 4455568999999999999 999987765
No 138
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=48.99 E-value=32 Score=26.39 Aligned_cols=34 Identities=9% Similarity=0.148 Sum_probs=28.4
Q ss_pred HHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 179 AYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 179 arAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
......|=-+++|.+||+++|+.|+.+--.+++-
T Consensus 23 ~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K 56 (201)
T COG1309 23 RLFAEKGYAATTVDEIAKAAGVSKGTLYRHFPSK 56 (201)
T ss_pred HHHHHcCcCCCCHHHHHHHhCCCcchhHHHcCCH
Confidence 3344579999999999999999999988887764
No 139
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=47.99 E-value=24 Score=26.66 Aligned_cols=25 Identities=20% Similarity=0.251 Sum_probs=22.6
Q ss_pred ccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 189 VSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
+++++||+.+|+.++.|=.+|.+++
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~~ 25 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGNG 25 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCC
Confidence 4789999999999999999998865
No 140
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=47.39 E-value=49 Score=29.46 Aligned_cols=44 Identities=16% Similarity=0.235 Sum_probs=34.9
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhh
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
..|+..|-+.|...|-. ....++||..+|++...|..+...-+.
T Consensus 174 ~~L~~~~r~il~l~y~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 174 ESLSEREQLVLSLYYYE-----ELNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred HhCCHHHHHHHHHHHhC-----CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46888999999988842 235689999999999999998765444
No 141
>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=46.74 E-value=19 Score=24.36 Aligned_cols=22 Identities=9% Similarity=0.138 Sum_probs=19.0
Q ss_pred HHHHHHHhCCChhhHHhhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFEDK 318 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQNR 318 (342)
..++|+.+|++.+.|..|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 5689999999999999996554
No 142
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=46.54 E-value=22 Score=25.26 Aligned_cols=24 Identities=13% Similarity=0.268 Sum_probs=21.0
Q ss_pred cccHHHHHHHhcCCHHHHHHHhcC
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+.+|+.||+++|+.+..+...++.
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~ 24 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKK 24 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 468999999999999999888764
No 143
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=46.47 E-value=33 Score=29.38 Aligned_cols=35 Identities=14% Similarity=0.171 Sum_probs=26.8
Q ss_pred HHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 176 RKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 176 ~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
++|..+|..+ =++|...||++||+.++.|..=++.
T Consensus 12 ~~Il~~Lq~d-~R~s~~eiA~~lglS~~tV~~Ri~r 46 (153)
T PRK11179 12 RGILEALMEN-ARTPYAELAKQFGVSPGTIHVRVEK 46 (153)
T ss_pred HHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3455566555 4579999999999999999876653
No 144
>PHA00675 hypothetical protein
Probab=46.28 E-value=36 Score=28.21 Aligned_cols=41 Identities=12% Similarity=0.198 Sum_probs=36.1
Q ss_pred hhhhchHHHHHHHHHH-HhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 167 EVRLKNWQLRKLAYAL-KTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 167 ~~~L~~WQl~rLarAL-~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
..+|..||++.+-+-+ +.|. |...||+.+|+.|+.|-...+
T Consensus 20 ~AKLt~~qV~~IR~l~~r~G~---s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 20 NAKLTDAEVERIRELHEVEGM---SYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred CcccCHHHHHHHHHHHHhcCc---cHHHHHHHhCCCHHHHHHHHc
Confidence 5689999999998888 7887 899999999999999976654
No 145
>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=46.18 E-value=20 Score=23.41 Aligned_cols=24 Identities=4% Similarity=0.343 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChhhHHhhhhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
..++|+.+|++++.|..|.++-..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 578999999999999999987553
No 146
>PRK10651 transcriptional regulator NarL; Provisional
Probab=45.62 E-value=30 Score=28.21 Aligned_cols=49 Identities=6% Similarity=0.041 Sum_probs=41.4
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
.||+.+.+.|+-..+. ...++||+.++++...|.+..+|=|.|-+|..+
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~~~ 203 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKLKSR 203 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCH
Confidence 3999999999886633 245677999999999999999999999998764
No 147
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=45.21 E-value=24 Score=32.11 Aligned_cols=49 Identities=10% Similarity=0.012 Sum_probs=43.0
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
.||+.|.+.|+-+.+- ..-.+||+.+++++..|..+.+|-..|.+|..+
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~nr 203 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKKIAVKNR 203 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence 4999999999999873 345778999999999999999999999999765
No 148
>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=44.74 E-value=55 Score=22.78 Aligned_cols=29 Identities=41% Similarity=0.495 Sum_probs=22.3
Q ss_pred HhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 183 KTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 183 ~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
..|..-.++++||..+|+.|..|-..|+.
T Consensus 20 ~~~~~~~~~~~la~~~~is~~~v~~~l~~ 48 (66)
T cd07377 20 KPGDRLPSERELAEELGVSRTTVREALRE 48 (66)
T ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34443355999999999999999877754
No 149
>smart00351 PAX Paired Box domain.
Probab=44.58 E-value=40 Score=28.39 Aligned_cols=36 Identities=19% Similarity=0.421 Sum_probs=28.1
Q ss_pred HHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 174 QLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 174 Ql~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
+..++-.+++.| .++..||+.||+.|..|-.|++.+
T Consensus 22 ~R~riv~~~~~G---~s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 22 ERQRIVELAQNG---VRPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred HHHHHHHHHHcC---CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 334444555666 488999999999999999999864
No 150
>PRK09526 lacI lac repressor; Reviewed
Probab=44.39 E-value=26 Score=31.86 Aligned_cols=28 Identities=14% Similarity=0.172 Sum_probs=25.1
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
.++++||+||+..|+.++.|=--|.+.+
T Consensus 3 ~~~~ti~dIA~~aGVS~~TVSrvLn~~~ 30 (342)
T PRK09526 3 SKPVTLYDVARYAGVSYQTVSRVLNQAS 30 (342)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHHhcCCC
Confidence 4679999999999999999999998765
No 151
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=43.77 E-value=7.7 Score=29.85 Aligned_cols=27 Identities=19% Similarity=0.468 Sum_probs=20.1
Q ss_pred HHHHHHHhCCChhhHHhhhhhhhhccCCCCCCC
Q 040593 297 ISSIVQVTNLPRRRIVKWFEDKRAEEGVPECRK 329 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R~ 329 (342)
...||+.+|++...|..| +..||..|+
T Consensus 12 ~~~lAkalGVs~~aVs~W------~~~IP~~ra 38 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW------GERIPAERA 38 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH------HTS--HHHH
T ss_pred HHHHHHHHCCCHHHHHHh------cCccCHHHH
Confidence 357999999999999999 567887764
No 152
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=43.40 E-value=21 Score=28.63 Aligned_cols=26 Identities=15% Similarity=0.239 Sum_probs=24.0
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
=-++|..+|+.||+-+..+.+|||+.
T Consensus 23 ~~~ti~~~AK~L~i~~~~l~~~Lr~~ 48 (111)
T PF03374_consen 23 GLYTIREAAKLLGIGRNKLFQWLREK 48 (111)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHhC
Confidence 56899999999999999999999984
No 153
>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=43.38 E-value=46 Score=24.70 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=25.3
Q ss_pred HHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 177 KLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 177 rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
++-+.|..|. +++++||..||+.|..|-.-++.
T Consensus 4 ~il~~L~~~~--~~~~eLa~~l~vS~~tv~~~l~~ 36 (69)
T TIGR00122 4 RLLALLADNP--FSGEKLGEALGMSRTAVNKHIQT 36 (69)
T ss_pred HHHHHHHcCC--cCHHHHHHHHCCCHHHHHHHHHH
Confidence 4455677663 67999999999999998766543
No 154
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=43.36 E-value=58 Score=22.24 Aligned_cols=23 Identities=43% Similarity=0.534 Sum_probs=20.0
Q ss_pred cc-cHHHHHHHhcCCHHHHHHHhc
Q 040593 188 KV-SVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 188 Kv-sIk~LA~EL~LDRa~VL~wLR 210 (342)
++ ++++||..+|+.|..|-..|+
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~ 42 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALS 42 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHH
Confidence 45 899999999999999977665
No 155
>PRK00215 LexA repressor; Validated
Probab=42.99 E-value=41 Score=29.73 Aligned_cols=30 Identities=23% Similarity=0.211 Sum_probs=25.0
Q ss_pred HHhcCccccHHHHHHHhcC-CHHHHHHHhcC
Q 040593 182 LKTGRRKVSVKSLAAELCL-DRAVVLEMLGD 211 (342)
Q Consensus 182 L~~GRRKvsIk~LA~EL~L-DRa~VL~wLR~ 211 (342)
+..+....++++||+.||+ +++.|-.+|+.
T Consensus 17 ~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 17 IEETGYPPSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred HHHhCCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 3566677899999999999 99999887653
No 156
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=42.77 E-value=35 Score=31.83 Aligned_cols=32 Identities=19% Similarity=0.196 Sum_probs=26.0
Q ss_pred HHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 179 AYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 179 arAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
-.++...++-+++++||++|||+++.|--+|.
T Consensus 31 L~~~~~~~~~~tl~eIa~~lglpkStv~RlL~ 62 (271)
T PRK10163 31 LQYLEKSGGSSSVSDISLNLDLPLSTTFRLLK 62 (271)
T ss_pred HHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 35566677779999999999999999966553
No 157
>PRK10072 putative transcriptional regulator; Provisional
Probab=42.64 E-value=21 Score=29.69 Aligned_cols=41 Identities=10% Similarity=0.117 Sum_probs=30.0
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhh
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
..+...+..|-.--..| ..+||..+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 34555666664333332 678999999999999999998874
No 158
>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=42.60 E-value=50 Score=27.23 Aligned_cols=37 Identities=16% Similarity=0.157 Sum_probs=27.8
Q ss_pred HHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 175 LRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 175 l~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
++.|..-...|...++++.||..||+.+..|-..|+.
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~ 48 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQ 48 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHH
Confidence 3444443345667899999999999999999776654
No 159
>PHA01083 hypothetical protein
Probab=42.23 E-value=28 Score=31.67 Aligned_cols=36 Identities=25% Similarity=0.265 Sum_probs=34.2
Q ss_pred HHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 176 RKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 176 ~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.+|-.|+|.-.--++-+.||..||+.|+.|=.|=+.
T Consensus 4 nkLLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~G 39 (149)
T PHA01083 4 NKLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTG 39 (149)
T ss_pred HHHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHcC
Confidence 578899999999999999999999999999999988
No 160
>PRK09480 slmA division inhibitor protein; Provisional
Probab=41.90 E-value=45 Score=27.90 Aligned_cols=26 Identities=19% Similarity=0.386 Sum_probs=24.9
Q ss_pred cCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 185 GRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 185 GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
| ..++|.+||++.|+.|+.+.-.+++
T Consensus 28 G-~~~ti~~Ia~~agvs~gt~Y~~F~~ 53 (194)
T PRK09480 28 G-ERITTAKLAARVGVSEAALYRHFPS 53 (194)
T ss_pred C-CccCHHHHHHHhCCCHhHHHHHCCC
Confidence 8 9999999999999999999998888
No 161
>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=41.39 E-value=50 Score=23.41 Aligned_cols=26 Identities=23% Similarity=0.275 Sum_probs=21.7
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
...+++++||..+|+.+..|-..|+.
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHH
Confidence 34689999999999999999776653
No 162
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI 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 Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=41.14 E-value=30 Score=31.44 Aligned_cols=26 Identities=23% Similarity=0.445 Sum_probs=23.3
Q ss_pred cccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
|++|++||+++|+.++.|=--|.+.+
T Consensus 1 ~~ti~dIA~~agVS~sTVSr~Ln~~~ 26 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNNEP 26 (311)
T ss_pred CCcHHHHHHHhCCCHHHHHHHhCCCC
Confidence 68999999999999999999997653
No 163
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=40.22 E-value=44 Score=23.49 Aligned_cols=41 Identities=17% Similarity=0.405 Sum_probs=29.6
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhh
Q 040593 271 QKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFE 316 (342)
Q Consensus 271 RTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQ 316 (342)
+..++..|++.+-..|..- ..+.+||+.+|++++.|.-++.
T Consensus 3 p~~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHHh
Confidence 3457777777777777654 4578899999999999988764
No 164
>PHA02591 hypothetical protein; Provisional
Probab=39.70 E-value=29 Score=29.03 Aligned_cols=32 Identities=22% Similarity=0.262 Sum_probs=26.1
Q ss_pred HHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 178 LAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 178 LarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
||+.|. ++-.+++.+|..||++...|-.+|++
T Consensus 51 vA~eL~--eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 51 VTHELA--RKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 455443 36689999999999999999999874
No 165
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=39.58 E-value=42 Score=23.65 Aligned_cols=41 Identities=15% Similarity=0.189 Sum_probs=21.6
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhh
Q 040593 271 QKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFE 316 (342)
Q Consensus 271 RTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQ 316 (342)
.+.||..|...++..+. ......+||..+|.+.+.|--|.+
T Consensus 2 ~~~Lt~~eR~~I~~l~~-----~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLE-----QGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHC-----S---HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHH-----cCCCHHHHHHHHCcCcHHHHHHHh
Confidence 46788889999988876 445677899999999999987754
No 166
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=39.26 E-value=60 Score=26.65 Aligned_cols=31 Identities=23% Similarity=0.198 Sum_probs=25.7
Q ss_pred HHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 178 LAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 178 LarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+.+.++.| .+++.+|+.||+.|+.|--+.|.
T Consensus 43 I~~ll~~G---~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 43 VAKMLKQG---KTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred HHHHHHCC---CCHHHHHHHHCcCHHHHHHHHHh
Confidence 33446666 49999999999999999999983
No 167
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=39.23 E-value=28 Score=25.31 Aligned_cols=20 Identities=5% Similarity=0.170 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChhhHHhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFE 316 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQ 316 (342)
+.++|+.+|+|.+.|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999943
No 168
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=39.04 E-value=37 Score=38.18 Aligned_cols=99 Identities=18% Similarity=0.243 Sum_probs=57.9
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhccc-CCCCCCCcccccccCCCcccccccccccCCCCCCCCCCCccc
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSAT-LPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEEPVHDR 264 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~-lpdE~~~~~~~~E~~~~~~v~~ets~~a~e~~~~~~lP~~~~ 264 (342)
--+--..++|.-.||.-++|-+|+-+- +.-+||.. .|. .|.+..|+.+.
T Consensus 581 ps~eelskia~qvglp~~vvk~wfE~~--~a~e~sv~rsps----------------------------~psg~~p~kv~ 630 (1007)
T KOG3623|consen 581 PSEEELSKIAQQVGLPFAVVKAWFEDE--EAEEMSVERSPS----------------------------QPSGERPVKVR 630 (1007)
T ss_pred CCHHHHHHHHHHhcccHHHHHHHHHhh--hhhhhhhccCcc----------------------------CCCCCCCcccc
Confidence 344456778889999999999998763 23344433 111 11111122211
Q ss_pred cccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 265 QHRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 265 q~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
+..+..+-.+|-.+|.-.-.|++..---++..+.....+++|||++|+..
T Consensus 631 -------sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsst 680 (1007)
T KOG3623|consen 631 -------SPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSST 680 (1007)
T ss_pred -------CCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCC
Confidence 22333334455566666555555544444555677788999999999865
No 169
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=39.00 E-value=39 Score=24.25 Aligned_cols=25 Identities=20% Similarity=0.377 Sum_probs=20.7
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+..+++.+|..+|++++.+-.|..+
T Consensus 11 ~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 11 KGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp CT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 4789999999999999999999988
No 170
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.92 E-value=37 Score=28.47 Aligned_cols=40 Identities=8% Similarity=0.185 Sum_probs=34.2
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhh
Q 040593 279 VKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 279 LetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
++.....|...+. .......||...|+++..|--+|.||-
T Consensus 16 l~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 16 LQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 4455566777778 999999999999999999999999986
No 171
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=38.86 E-value=29 Score=24.10 Aligned_cols=23 Identities=17% Similarity=0.245 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChhhHHhhhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQNRR 319 (342)
..+||..+|++...|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47899999999999999999854
No 172
>PRK13239 alkylmercury lyase; Provisional
Probab=38.41 E-value=61 Score=30.60 Aligned_cols=42 Identities=36% Similarity=0.293 Sum_probs=37.7
Q ss_pred chHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 171 KNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 171 ~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
..|=...|.|.|+.|| -++|..||+.+|.+-..|.+.|...+
T Consensus 20 ~~~~~~~llr~la~G~-pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 20 TATLLVPLLRLLAKGR-PVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred chHHHHHHHHHHHcCC-CCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 4678889999999885 79999999999999999999999865
No 173
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=38.29 E-value=25 Score=24.71 Aligned_cols=43 Identities=12% Similarity=0.214 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 274 LKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 274 FT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
++..|-..+.-.| -......++|..+|++.+.|++|.+.=|.+
T Consensus 11 L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 4444555555443 456678899999999999999999865543
No 174
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=38.28 E-value=40 Score=24.97 Aligned_cols=27 Identities=19% Similarity=0.332 Sum_probs=24.3
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
.+..+..+||+.+|+.++.|-.|+.+.
T Consensus 16 ~~~~t~~~lA~~~gis~~tis~~~~g~ 42 (78)
T TIGR02607 16 PLGLSIRALAKALGVSRSTLSRIVNGR 42 (78)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 467889999999999999999999874
No 175
>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=38.24 E-value=30 Score=23.58 Aligned_cols=23 Identities=13% Similarity=0.076 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChhhHHhhhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQNRR 319 (342)
.++||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999998775
No 176
>PF13730 HTH_36: Helix-turn-helix domain
Probab=38.13 E-value=82 Score=22.10 Aligned_cols=42 Identities=10% Similarity=0.106 Sum_probs=28.4
Q ss_pred cCCHHHHHHHHHHhhhc-----CCCCHHHHHHHHHHhCCChhhHHhhhhh
Q 040593 273 RLKKVQVKTLEMVYRRS-----KRPTDAMISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 273 rFT~~QLetLErvF~rT-----~YPdv~~RE~LA~~t~LpesrVQVWFQN 317 (342)
.++..+...+=-..... -|| ..+.||..+|++++.|+.+.+.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~p---S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFP---SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCc---CHHHHHHHHCcCHHHHHHHHHH
Confidence 34555554444333332 455 4788999999999999998865
No 177
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=37.90 E-value=84 Score=33.19 Aligned_cols=108 Identities=18% Similarity=0.190 Sum_probs=62.9
Q ss_pred cCccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhcccCC--CCCCCcccccccCCCcccccccccccCCCCCCCCCCCc
Q 040593 185 GRRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLP--DKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEEPVH 262 (342)
Q Consensus 185 GRRKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~lp--dE~~~~~~~~E~~~~~~v~~ets~~a~e~~~~~~lP~~ 262 (342)
|| .-++..||++||++-..|..+++.... .+|.--| ++... ..++.+..+ ....|..
T Consensus 372 gr-~PT~eELAe~Lgis~e~V~~~~~~~~~---~~SLD~~i~~d~~~-------~l~d~l~D~----------~~~~p~~ 430 (509)
T PRK05901 372 GR-EPTPEELAKEMGFTPEKVREIQKYNRE---PISLDKTIGKEGDS-------QFGDFIEDS----------EAVSPVD 430 (509)
T ss_pred CC-CCCHHHHHHHhCCCHHHHHHHHHhcCC---CcccccccccCCcc-------cHHHhccCC----------CCCCHHH
Confidence 54 455899999999999999999876431 2332211 11100 011111110 0011211
Q ss_pred cccc------cccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhh
Q 040593 263 DRQH------RWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKW 314 (342)
Q Consensus 263 ~~q~------~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVW 314 (342)
.... -+..=..|+.-+-..|...|.-..|.. ...++||+.+|+++.||..-
T Consensus 431 ~~~~~~l~~~L~~aL~~L~eREr~VI~lRyGL~~~e~-~TL~EIa~~lGVSrERVRQI 487 (509)
T PRK05901 431 AVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQP-KTLDEIGQVYGVTRERIRQI 487 (509)
T ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHHhhccCCCC-CCHHHHHHHHCCCHHHHHHH
Confidence 1100 011113789999999999997655533 46789999999999999764
No 178
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=37.84 E-value=31 Score=23.81 Aligned_cols=26 Identities=19% Similarity=0.408 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhCCChhhHHhhhhhhh
Q 040593 294 DAMISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 294 v~~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
.....++|+.+|+++..|..|.+.=+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 45678899999999999999987533
No 179
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=37.82 E-value=89 Score=20.99 Aligned_cols=22 Identities=23% Similarity=0.175 Sum_probs=20.3
Q ss_pred ccHHHHHHHhcCCHHHHHHHhc
Q 040593 189 VSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR 210 (342)
.+++++|..|++.+..|-.+++
T Consensus 16 ~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 16 KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5999999999999999998876
No 180
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=37.04 E-value=40 Score=22.43 Aligned_cols=24 Identities=25% Similarity=0.268 Sum_probs=20.4
Q ss_pred cccHHHHHHHhcCCHHHHHHHhcC
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.+++++||..||+.+..|-..|+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~ 31 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKR 31 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHH
Confidence 368899999999999999777654
No 181
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=36.95 E-value=52 Score=28.27 Aligned_cols=32 Identities=9% Similarity=0.129 Sum_probs=27.6
Q ss_pred HHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 180 YALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 180 rAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
...+.|-..|+|.+||++.|+.++.+...+.+
T Consensus 23 lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~F~s 54 (213)
T PRK09975 23 QFALRGVSNTTLNDIADAANVTRGAIYWHFEN 54 (213)
T ss_pred HHHHcCcccCCHHHHHHHcCCCHHHHHHHcCC
Confidence 34578999999999999999999998877755
No 182
>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=36.86 E-value=53 Score=23.00 Aligned_cols=32 Identities=28% Similarity=0.343 Sum_probs=23.7
Q ss_pred HHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 177 KLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 177 rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
++-.+|.. ...++.+||+.||+++..|-.-|+
T Consensus 6 ~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~ 37 (47)
T PF01022_consen 6 RILKLLSE--GPLTVSELAEELGLSQSTVSHHLK 37 (47)
T ss_dssp HHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHh--CCCchhhHHHhccccchHHHHHHH
Confidence 44556666 458899999999999999965553
No 183
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=36.75 E-value=81 Score=29.18 Aligned_cols=44 Identities=23% Similarity=0.271 Sum_probs=33.7
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhh
Q 040593 271 QKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 271 RTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
-..|+..|-..|...|.. .....+||..+|+|...|..+...-+
T Consensus 210 l~~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~ 253 (268)
T PRK06288 210 IKTLPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAV 253 (268)
T ss_pred HHhCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 346888888888887742 34578999999999999998875433
No 184
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=36.52 E-value=40 Score=30.76 Aligned_cols=51 Identities=14% Similarity=0.185 Sum_probs=43.5
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 271 QKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 271 RTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
...||..|.++|.-+. ....-.+||+.+|++++.|..+.+|=+.|-++..+
T Consensus 169 ~~~Lt~re~evl~~~a------~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 169 AGVLSEREREVLAWTA------LGRRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hccCCHHHHHHHHHHH------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 3479999999999864 33667888999999999999999999999988754
No 185
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=36.15 E-value=32 Score=26.13 Aligned_cols=22 Identities=23% Similarity=0.481 Sum_probs=18.9
Q ss_pred HHHHHHHHHhCCChhhHHhhhh
Q 040593 295 AMISSIVQVTNLPRRRIVKWFE 316 (342)
Q Consensus 295 ~~RE~LA~~t~LpesrVQVWFQ 316 (342)
....+||+.+|+|.+.|+.|-+
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH
Confidence 3467899999999999999964
No 186
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=35.80 E-value=42 Score=27.65 Aligned_cols=43 Identities=9% Similarity=0.066 Sum_probs=34.1
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhh
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
..|++.|.+.|...|- ......+||+.+|+|+..|..|.+.-+
T Consensus 127 ~~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~ 169 (182)
T PRK09652 127 ESLPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAR 169 (182)
T ss_pred HhCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3688999999988764 233567889999999999999988433
No 187
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=35.59 E-value=78 Score=28.12 Aligned_cols=30 Identities=17% Similarity=0.379 Sum_probs=27.0
Q ss_pred HhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 183 KTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 183 ~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
+...|.++|..|+.++|++-..|+.|+|+-
T Consensus 41 ~~p~~~ati~eV~e~tgVs~~~I~~~IreG 70 (137)
T TIGR03826 41 KHENRQATVSEIVEETGVSEKLILKFIREG 70 (137)
T ss_pred HCCCCCCCHHHHHHHHCcCHHHHHHHHHcC
Confidence 456678999999999999999999999984
No 188
>PF13518 HTH_28: Helix-turn-helix domain
Probab=35.54 E-value=37 Score=23.21 Aligned_cols=25 Identities=16% Similarity=0.461 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCChhhHHhhhhhhhh
Q 040593 296 MISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 296 ~RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
...++|..+||+.+.|..|.+.=+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 4567999999999999999987775
No 189
>PF13730 HTH_36: Helix-turn-helix domain
Probab=35.54 E-value=39 Score=23.80 Aligned_cols=23 Identities=26% Similarity=0.358 Sum_probs=20.4
Q ss_pred ccHHHHHHHhcCCHHHHHHHhcC
Q 040593 189 VSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.|++.||..+|+.|..|...++.
T Consensus 26 pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHH
Confidence 38999999999999999988763
No 190
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=35.21 E-value=54 Score=30.81 Aligned_cols=43 Identities=23% Similarity=0.295 Sum_probs=35.4
Q ss_pred hH--HHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCCC
Q 040593 172 NW--QLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPPP 214 (342)
Q Consensus 172 ~W--Ql~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ppP 214 (342)
+| -+.+.|-|+++-+---.|..||.|||..+++|...|+.-+.
T Consensus 43 TWvdSLavAAga~arekag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 43 TWVDSLAVAAGALAREKAGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred chhhHHHHHHHHHHHHHccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 55 36677777777666678999999999999999999998665
No 191
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=34.75 E-value=42 Score=29.82 Aligned_cols=45 Identities=13% Similarity=0.160 Sum_probs=36.8
Q ss_pred cccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 271 QKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 271 RTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
.+.||..|.+.|...+ .....++||..+|+++..|..|-++.+.+
T Consensus 4 ~~~Lt~rqreVL~lr~------~GlTq~EIAe~LGiS~~tVs~ie~ra~kk 48 (141)
T PRK03975 4 ESFLTERQIEVLRLRE------RGLTQQEIADILGTSRANVSSIEKRAREN 48 (141)
T ss_pred ccCCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4679999999998832 33457789999999999999999876655
No 192
>PF05285 SDA1: SDA1; InterPro: IPR007949 This domain consists of several SDA1 protein homologues. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localised in the nucleus [].
Probab=34.58 E-value=26 Score=34.34 Aligned_cols=18 Identities=28% Similarity=0.073 Sum_probs=11.0
Q ss_pred CCcHHHHHHHHHHHhhcC
Q 040593 85 EDDPFEALFSLLEEDLKN 102 (342)
Q Consensus 85 d~da~E~LF~~LEeDLkn 102 (342)
.-.++|.|...+++.-..
T Consensus 67 ~i~G~elL~~~~~~~~~~ 84 (324)
T PF05285_consen 67 GIPGAELLEEWKEEERKD 84 (324)
T ss_pred CCChHHHHHHHhhcchhh
Confidence 445788777776554433
No 193
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=34.46 E-value=58 Score=30.13 Aligned_cols=30 Identities=30% Similarity=0.220 Sum_probs=23.3
Q ss_pred HHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 181 ALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 181 AL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
++.....-+++++||+.||++|+.|-.+|+
T Consensus 19 ~l~~~~~~ls~~eia~~lgl~kstv~RlL~ 48 (263)
T PRK09834 19 ALNRLDGGATVGLLAELTGLHRTTVRRLLE 48 (263)
T ss_pred HHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344445559999999999999999966553
No 194
>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=34.28 E-value=52 Score=24.32 Aligned_cols=37 Identities=27% Similarity=0.306 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhh
Q 040593 276 KVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFE 316 (342)
Q Consensus 276 ~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQ 316 (342)
.-|++.|+-.|. +++.+.. +||..+|++++.|+.-..
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 358889999999 7777655 899999999999986543
No 195
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=34.20 E-value=53 Score=30.11 Aligned_cols=24 Identities=17% Similarity=0.480 Sum_probs=20.7
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhc
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
+.+++++||++|||.++.|..+|+
T Consensus 27 ~~l~l~eia~~lgl~kstv~Rll~ 50 (257)
T PRK15090 27 REIGITELSQRVMMSKSTVYRFLQ 50 (257)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHH
Confidence 468999999999999999976653
No 196
>PRK04217 hypothetical protein; Provisional
Probab=34.01 E-value=71 Score=27.33 Aligned_cols=45 Identities=9% Similarity=0.060 Sum_probs=36.2
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
..++..|.+.+...|.... ..++||+.+|+++..|...+..-|.+
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 3688999888887775433 67889999999999999998865554
No 197
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=33.81 E-value=71 Score=28.26 Aligned_cols=32 Identities=22% Similarity=0.280 Sum_probs=26.0
Q ss_pred HHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 179 AYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 179 arAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
...+..| .|+..+|+.||+.|+.|.-+++..+
T Consensus 166 ~~~~~~g---~s~~~iak~lgis~~Tv~r~~k~~~ 197 (200)
T PRK13413 166 KKLLDKG---TSKSEIARKLGVSRTTLARFLKTRG 197 (200)
T ss_pred HHHHHCC---CCHHHHHHHHCCCHHHHHHHHHhcc
Confidence 3345556 5999999999999999999998643
No 198
>PRK10870 transcriptional repressor MprA; Provisional
Probab=33.80 E-value=73 Score=28.17 Aligned_cols=44 Identities=9% Similarity=0.047 Sum_probs=34.9
Q ss_pred hhhhchHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 167 EVRLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 167 ~~~L~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
+..|..+|...|..-...|-..++.++||..||++++.|=..+.
T Consensus 50 ~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~ 93 (176)
T PRK10870 50 AQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIAD 93 (176)
T ss_pred HCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 44577788888876666667788999999999999999866654
No 199
>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=33.61 E-value=78 Score=22.65 Aligned_cols=31 Identities=19% Similarity=0.310 Sum_probs=21.0
Q ss_pred HHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 181 ALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 181 AL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
++....+..++++||..|+++++.|-..++.
T Consensus 11 ~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~ 41 (68)
T PF13463_consen 11 ALAHSDGPMTQSDLAERLGISKSTVSRIIKK 41 (68)
T ss_dssp HHT--TS-BEHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHccCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3445667778899999999999999887763
No 200
>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=33.08 E-value=57 Score=27.13 Aligned_cols=29 Identities=21% Similarity=0.342 Sum_probs=25.3
Q ss_pred HHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 179 AYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 179 arAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
-.+++.|. ||.++|+.+|+.++.|..|++
T Consensus 12 l~~~~~g~---s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 12 LAYIEKGK---SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHHccc---hHHHHHHHhCcHHHHHHHHHH
Confidence 34666666 999999999999999999998
No 201
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.01 E-value=72 Score=25.80 Aligned_cols=33 Identities=18% Similarity=0.221 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCccccHHHHHHHhcC-CHHHHHHHhcC
Q 040593 176 RKLAYALKTGRRKVSVKSLAAELCL-DRAVVLEMLGD 211 (342)
Q Consensus 176 ~rLarAL~~GRRKvsIk~LA~EL~L-DRa~VL~wLR~ 211 (342)
+..+.++..| .+|..||+++|+ ....+-.|.+.
T Consensus 15 ~iv~~~~~~g---~sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 15 EAVALYLRGG---DTVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred HHHHHHHhcC---ccHHHHHHHhCCCChHHHHHHHHH
Confidence 3444455455 499999999996 99999999885
No 202
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=32.89 E-value=52 Score=25.37 Aligned_cols=44 Identities=11% Similarity=0.218 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
.++..|...+...|-. .+ ...+||..+|+|++.|..|.+.-+.+
T Consensus 110 ~L~~~~~~ii~~~~~~-g~----s~~eIA~~l~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-GL----SYKEIAEILGISVGTVKRRLKRARKK 153 (158)
T ss_pred hCCHHHHHHHhhHHhc-CC----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 6778888887766542 23 45688999999999999998876554
No 203
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=32.88 E-value=40 Score=23.21 Aligned_cols=21 Identities=24% Similarity=0.309 Sum_probs=19.4
Q ss_pred HHHHHhcCCHHHHHHHhcCCC
Q 040593 193 SLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 193 ~LA~EL~LDRa~VL~wLR~pp 213 (342)
+||+.+|+.++.|-.||++++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 689999999999999999974
No 204
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=32.69 E-value=56 Score=29.46 Aligned_cols=42 Identities=12% Similarity=0.332 Sum_probs=37.4
Q ss_pred cCCHHHHHHHHHHhhhc--CCCCHHHHHHHHHHhCCChhhHHhh
Q 040593 273 RLKKVQVKTLEMVYRRS--KRPTDAMISSIVQVTNLPRRRIVKW 314 (342)
Q Consensus 273 rFT~~QLetLErvF~rT--~YPdv~~RE~LA~~t~LpesrVQVW 314 (342)
.||..|++.|..+|..- -||-......||+.+|++.+.++.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~eh 198 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEH 198 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHH
Confidence 79999999999999876 5698999999999999999887643
No 205
>PF07093 SGT1: SGT1 protein; InterPro: IPR010770 This family consists of several eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known to suppress GCR2 and is highly expressed in the muscle and heart. The function of this family is unknown although it has been speculated that SGT1 may be functionally analogous to the Gcr2p protein of Saccharomyces cerevisiae which is known to be a regulatory factor of glycolytic gene expression [].
Probab=32.37 E-value=1.2e+02 Score=32.09 Aligned_cols=20 Identities=35% Similarity=0.428 Sum_probs=13.8
Q ss_pred CCCCHHHHHHHHHHHHHHhCC
Q 040593 112 EEIDEEDLDKLATELAEALGD 132 (342)
Q Consensus 112 d~iseed~a~~e~el~~a~gd 132 (342)
.+|+. |...|-+.|.++||-
T Consensus 472 ~~v~f-D~d~F~~~l~~~Lg~ 491 (589)
T PF07093_consen 472 EDVSF-DEDEFLKMLREMLGL 491 (589)
T ss_pred Ccccc-CHHHHHHHHHHHcCC
Confidence 34443 566777799999993
No 206
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=32.30 E-value=1.1e+02 Score=31.64 Aligned_cols=120 Identities=15% Similarity=0.148 Sum_probs=70.3
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhccc--CCCCCCCcccccccCCCcccccccccccCCCCCCCCCCCccc
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSAT--LPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEEPVHDR 264 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~--lpdE~~~~~~~~E~~~~~~v~~ets~~a~e~~~~~~lP~~~~ 264 (342)
|..++..||++||++-..|-++++..+. .+|.- +.++... ..++.+.. ....|-...
T Consensus 277 R~pt~~EiA~~l~is~~~vr~~l~~~~~---~~SLd~~vg~~~d~-------~l~d~l~~-----------~~~~pee~~ 335 (415)
T PRK07598 277 RTPTIEDIAQELEMTPTQVREVLLRVPR---SVSLETKVGKDKDT-------ELGDLLET-----------DDISPEEML 335 (415)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHccC---CcccccccCCCccc-------cHHHhccC-----------CCCCHHHHH
Confidence 4466899999999999999999987542 12211 1111100 00000000 000010000
Q ss_pred ---ccc---ccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCC
Q 040593 265 ---QHR---WSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECR 328 (342)
Q Consensus 265 ---q~~---w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R 328 (342)
... ...=..++..|-++|.-.|.-.-.- ....++||..+|+|+.+|..+-..-+.|-+-|.++
T Consensus 336 ~~~~l~~~L~~~L~~L~~reR~VI~LRygl~d~~-~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~~~~ 404 (415)
T PRK07598 336 MRESLQRDLQHLLADLTSRERDVIRMRFGLADGH-TYSLAEIGRALDLSRERVRQIESKALQKLRQPKRR 404 (415)
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHhcCCCC-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHhchhHH
Confidence 000 0111358899999999888632211 12468999999999999999988777777766654
No 207
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=31.76 E-value=83 Score=25.84 Aligned_cols=51 Identities=6% Similarity=0.074 Sum_probs=44.2
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCC
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECR 328 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R 328 (342)
..||+.+.+.|+-..+.. .+++||+.++++.+.|.+--.+=|.|-++.++.
T Consensus 142 ~~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~~~~ 192 (204)
T PRK09958 142 DSLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEKLECKSLM 192 (204)
T ss_pred ccCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHH
Confidence 359999999999888654 478999999999999999999999999987754
No 208
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=31.50 E-value=1e+02 Score=25.56 Aligned_cols=39 Identities=10% Similarity=0.169 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 173 WQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 173 WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+-...+..-.+.|=..++|..||++.|+.++.+-..+++
T Consensus 13 Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~~ly~~F~s 51 (189)
T TIGR03384 13 LIDATIESIGERGSLDVTIAQIARRAGVSSGIISHYFGG 51 (189)
T ss_pred HHHHHHHHHHhcCcccCCHHHHHHHhCCCHHHHHHHcCC
Confidence 334445555688999999999999999999998887754
No 209
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=31.12 E-value=77 Score=26.96 Aligned_cols=33 Identities=12% Similarity=0.098 Sum_probs=28.6
Q ss_pred HHHhcCccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 181 ALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 181 AL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
-.+.|=.++||.+||++.|+.++.+-..+++-.
T Consensus 21 f~e~G~~~~s~~~IA~~agvs~~~lY~hF~sKe 53 (202)
T TIGR03613 21 FSRFGFHGTSLEQIAELAGVSKTNLLYYFPSKD 53 (202)
T ss_pred HHHhCcccCCHHHHHHHhCCCHHHHHHHcCCHH
Confidence 346899999999999999999999988887643
No 210
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=30.97 E-value=79 Score=28.63 Aligned_cols=39 Identities=15% Similarity=0.252 Sum_probs=31.8
Q ss_pred HHHHHHHHH----hcCccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 175 LRKLAYALK----TGRRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 175 l~rLarAL~----~GRRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
.+.|+.|+. .|=-.+||..||++||+.+.-+--.++|-.
T Consensus 7 e~Il~aA~~l~~e~G~~~lsmr~lA~~lgv~~~slY~hf~~K~ 49 (205)
T PRK13756 7 EKVIDSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKR 49 (205)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchHHHHHcCCHH
Confidence 345566665 799999999999999999999988887643
No 211
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=30.86 E-value=37 Score=26.50 Aligned_cols=20 Identities=20% Similarity=0.393 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCChhhHHhhh
Q 040593 296 MISSIVQVTNLPRRRIVKWF 315 (342)
Q Consensus 296 ~RE~LA~~t~LpesrVQVWF 315 (342)
.-..||..+|+++.+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 34578999999999999994
No 212
>PRK09726 antitoxin HipB; Provisional
Probab=30.70 E-value=98 Score=24.28 Aligned_cols=28 Identities=14% Similarity=0.281 Sum_probs=25.4
Q ss_pred cCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 185 GRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 185 GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
.++..+.+.||+.+|+.++.|-.|.++.
T Consensus 22 ~~~gltq~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 22 QQNGWTQSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHCCC
Confidence 4668999999999999999999999974
No 213
>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=30.54 E-value=82 Score=24.34 Aligned_cols=36 Identities=31% Similarity=0.388 Sum_probs=24.3
Q ss_pred HHHHHHHHHhcCcc-ccHHHHHHHhcCCHHHHHHHhc
Q 040593 175 LRKLAYALKTGRRK-VSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 175 l~rLarAL~~GRRK-vsIk~LA~EL~LDRa~VL~wLR 210 (342)
++.|..-...+..+ +++++||+.+++....|-..|.
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34444433344444 9999999999999988776654
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=30.47 E-value=80 Score=24.61 Aligned_cols=32 Identities=19% Similarity=0.327 Sum_probs=22.2
Q ss_pred HHhcCccccHHHHHHHhcCCHH-HHHHHhcCCC
Q 040593 182 LKTGRRKVSVKSLAAELCLDRA-VVLEMLGDPP 213 (342)
Q Consensus 182 L~~GRRKvsIk~LA~EL~LDRa-~VL~wLR~pp 213 (342)
++.-..-++|.+|..+|.+|-. .+++||+++|
T Consensus 14 mK~r~~Plt~~eI~d~l~~d~~~~~~~~Lk~np 46 (65)
T PF02186_consen 14 MKKRDHPLTLEEILDYLSLDIGKKLKQWLKNNP 46 (65)
T ss_dssp HHHH-S-B-HHHHHHHHTSSS-HHHHHHHHH-T
T ss_pred HHhcCCCcCHHHHHHHHcCCCCHHHHHHHHcCC
Confidence 4444677899999999999864 5788999766
No 215
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=30.40 E-value=77 Score=21.26 Aligned_cols=26 Identities=27% Similarity=0.257 Sum_probs=22.4
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
...+++.+|++.||+.+..|-..|+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 56689999999999999998887764
No 216
>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=30.14 E-value=59 Score=21.90 Aligned_cols=22 Identities=9% Similarity=-0.070 Sum_probs=20.2
Q ss_pred cHHHHHHHhcCCHHHHHHHhcC
Q 040593 190 SVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 190 sIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+++++|+-||+....|-.|.+.
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHC
Confidence 6899999999999999999766
No 217
>PRK00767 transcriptional regulator BetI; Validated
Probab=30.10 E-value=1.1e+02 Score=25.75 Aligned_cols=30 Identities=10% Similarity=0.240 Sum_probs=26.9
Q ss_pred HHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 182 LKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 182 L~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.+.|=..++|..||++.|+.++.+...+.+
T Consensus 23 ~~~G~~~~s~~~Ia~~aGvs~gslY~~F~~ 52 (197)
T PRK00767 23 GEVGLLDATIAQIARRAGVSTGIISHYFGG 52 (197)
T ss_pred HHcCcccCCHHHHHHHhCCCHHHHHHHhCC
Confidence 578999999999999999999999888744
No 218
>PRK09483 response regulator; Provisional
Probab=29.95 E-value=73 Score=26.46 Aligned_cols=51 Identities=10% Similarity=0.146 Sum_probs=41.3
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCC
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECR 328 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R 328 (342)
..||+.+.+.|.-...- + ...+||+.++++++.|..--+|=+.|-+|..+.
T Consensus 147 ~~Lt~rE~~vl~~~~~G--~----~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~~ 197 (217)
T PRK09483 147 ASLSERELQIMLMITKG--Q----KVNEISEQLNLSPKTVNSYRYRMFSKLNISGDV 197 (217)
T ss_pred cccCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHH
Confidence 45999999999755322 2 334899999999999999999999999997654
No 219
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=29.93 E-value=47 Score=24.60 Aligned_cols=23 Identities=13% Similarity=0.381 Sum_probs=20.6
Q ss_pred HHHHHHHhCCChhhHHhhhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQNRR 319 (342)
.++||..+|++...|..|..+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999998775
No 220
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=29.59 E-value=56 Score=22.69 Aligned_cols=38 Identities=18% Similarity=0.192 Sum_probs=26.0
Q ss_pred chHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 171 KNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 171 ~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
+.-....|..||+.-. =++...|+.||+.|..+-.-|+
T Consensus 3 ~~~E~~~i~~aL~~~~--gn~~~aA~~Lgisr~tL~~klk 40 (42)
T PF02954_consen 3 EEFEKQLIRQALERCG--GNVSKAARLLGISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHHHHTT--T-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhC--CCHHHHHHHHCCCHHHHHHHHH
Confidence 3344566778887543 3578999999999998876554
No 221
>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=29.56 E-value=68 Score=21.31 Aligned_cols=19 Identities=26% Similarity=0.337 Sum_probs=15.7
Q ss_pred cHHHHHHHhcCCHHHHHHH
Q 040593 190 SVKSLAAELCLDRAVVLEM 208 (342)
Q Consensus 190 sIk~LA~EL~LDRa~VL~w 208 (342)
.|..+|+++|+.|+.++..
T Consensus 13 ~l~~~a~~~g~s~s~~ir~ 31 (39)
T PF01402_consen 13 RLDELAKELGRSRSELIRE 31 (39)
T ss_dssp HHHHHHHHHTSSHHHHHHH
T ss_pred HHHHHHHHHCcCHHHHHHH
Confidence 3678999999999988753
No 222
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=29.54 E-value=49 Score=31.67 Aligned_cols=15 Identities=27% Similarity=0.184 Sum_probs=10.7
Q ss_pred ccCccchhcccCCCC
Q 040593 19 RLSPSQYLRLFPGHH 33 (342)
Q Consensus 19 ~~~~~~~~~~~~~~~ 33 (342)
.+|..+--|.+|||.
T Consensus 25 ~~S~~~ssRdLPsHT 39 (244)
T PF04889_consen 25 VPSKQYSSRDLPSHT 39 (244)
T ss_pred ccccccccccCCcCC
Confidence 345566679999994
No 223
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=29.53 E-value=58 Score=23.64 Aligned_cols=23 Identities=13% Similarity=0.111 Sum_probs=20.6
Q ss_pred cHHHHHHHhcCCHHHHHHHhcCC
Q 040593 190 SVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 190 sIk~LA~EL~LDRa~VL~wLR~p 212 (342)
+|+++|+.+|+.+..|--|.+..
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTT
T ss_pred cHHHHHHHHCcCHHHHHHHHHhc
Confidence 68999999999999999997753
No 224
>PF12728 HTH_17: Helix-turn-helix domain
Probab=29.34 E-value=51 Score=22.95 Aligned_cols=24 Identities=8% Similarity=0.484 Sum_probs=20.7
Q ss_pred HHHHHHHhCCChhhHHhhhhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
.+++|+.+|++++.|..|-++..-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 578999999999999999976643
No 225
>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=29.30 E-value=66 Score=26.22 Aligned_cols=29 Identities=24% Similarity=0.322 Sum_probs=24.7
Q ss_pred HhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 183 KTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 183 ~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
..|+..++++.||..||+.+..|-..|+.
T Consensus 20 ~~~~~~~s~~eia~~~~i~~~~v~~il~~ 48 (132)
T TIGR00738 20 NPDEGPVSVKEIAERQGISRSYLEKILRT 48 (132)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHH
Confidence 35566899999999999999999887765
No 226
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=29.15 E-value=91 Score=22.69 Aligned_cols=29 Identities=14% Similarity=0.377 Sum_probs=15.2
Q ss_pred HhhhcC-CCCHHHHHHHHHHhCCChhhHHh
Q 040593 285 VYRRSK-RPTDAMISSIVQVTNLPRRRIVK 313 (342)
Q Consensus 285 vF~rT~-YPdv~~RE~LA~~t~LpesrVQV 313 (342)
+-.-.. .|+......|+..+|++...++-
T Consensus 34 iE~G~~~~p~~~~l~~l~~~l~~~~~~~~~ 63 (64)
T PF13560_consen 34 IERGRRPRPSPDTLQRLARALGVPPDERAE 63 (64)
T ss_dssp HHTTSSSS-BHHHHHHHHHHTT--HHHHHC
T ss_pred HHCCCCCCCCHHHHHHHHHHHCcCHHHHcc
Confidence 333444 36677777777777776665543
No 227
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=29.13 E-value=61 Score=29.85 Aligned_cols=26 Identities=15% Similarity=0.321 Sum_probs=23.2
Q ss_pred cccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
+++|++||+.+|+.++.|=--|.+.+
T Consensus 1 ~~ti~dIA~~aGVS~~TVSrvLn~~~ 26 (346)
T PRK10401 1 MITIRDVARQAGVSVATVSRVLNNSA 26 (346)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHCCCC
Confidence 37899999999999999999997754
No 228
>PLN02543 pfkB-type carbohydrate kinase family protein
Probab=29.07 E-value=1.1e+02 Score=32.12 Aligned_cols=15 Identities=33% Similarity=0.372 Sum_probs=7.2
Q ss_pred CccchhcccCCCCCC
Q 040593 21 SPSQYLRLFPGHHRK 35 (342)
Q Consensus 21 ~~~~~~~~~~~~~~~ 35 (342)
..+|-++.||--+..
T Consensus 26 ~~~~~~~~~~~~~~~ 40 (496)
T PLN02543 26 RSSQKTRRFPKPKAS 40 (496)
T ss_pred ccccccccCCCCCcc
Confidence 344445556554433
No 229
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=28.83 E-value=70 Score=26.10 Aligned_cols=39 Identities=26% Similarity=0.285 Sum_probs=32.0
Q ss_pred HHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC-CCch
Q 040593 178 LAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP-PPNL 216 (342)
Q Consensus 178 LarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p-pP~l 216 (342)
+..|++.-|++-.+..||+..|+.|+.+-.|.++. .|.+
T Consensus 33 ~~~~l~~~r~~~glSqLAe~~GIs~stLs~iE~g~~~Ps~ 72 (89)
T TIGR02684 33 IAHALGYIARARGMTQLARKTGLSRESLYKALSGKGNPTF 72 (89)
T ss_pred HHHHHHHHHHHCChHHHHHHHCCCHHHHHHHHcCCCCCCH
Confidence 56667777888888889999999999999999884 3443
No 230
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=28.31 E-value=1.2e+02 Score=26.78 Aligned_cols=65 Identities=14% Similarity=0.048 Sum_probs=46.1
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhh--------hhccCCCCCCCccccCCCcc
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDK--------RAEEGVPECRKPFQRSDPKT 338 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNR--------RAKd~vp~~R~~~qrs~~et 338 (342)
.+|..+++.|-.....+ |=....-++||..+|+++..|+.-+++= |.++|..-+=+=|+|-..|.
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 230 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIHYGVTGRPVYRYRLQAEH 230 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEeeccCCCCCCeeeeccccc
Confidence 37888887776655433 4455677999999999999999999986 77776655444444444443
No 231
>PHA01976 helix-turn-helix protein
Probab=27.81 E-value=56 Score=23.66 Aligned_cols=23 Identities=17% Similarity=0.247 Sum_probs=20.4
Q ss_pred HHHHHHHhCCChhhHHhhhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQNRR 319 (342)
..+||..+|++.+.|..|..+++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 57899999999999999987764
No 232
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=27.52 E-value=46 Score=30.92 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=19.8
Q ss_pred cccHHHHHHHhcCCHHHHHHHhc
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR 210 (342)
-+++..||++.|.||.+|.+-.+
T Consensus 41 EI~~t~iAka~gVdRrvV~~Ti~ 63 (167)
T COG2150 41 EIPITKIAKATGVDRRVVYATIE 63 (167)
T ss_pred EechHHHHHHhCcchHhHHHHHH
Confidence 57899999999999999986543
No 233
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=27.27 E-value=3.4e+02 Score=24.93 Aligned_cols=41 Identities=15% Similarity=0.204 Sum_probs=32.4
Q ss_pred ccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhh
Q 040593 270 AQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWF 315 (342)
Q Consensus 270 kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWF 315 (342)
.-..|+..+-..+...|- ......+||..+|++..+|...-
T Consensus 203 ~l~~L~~rer~vi~~~~~-----~~~t~~eIA~~lgis~~~V~~~~ 243 (254)
T TIGR02850 203 AMKRLNEREKMILNMRFF-----EGKTQMEVAEEIGISQAQVSRLE 243 (254)
T ss_pred HHHcCCHHHHHHHHHHHc-----CCCCHHHHHHHHCcCHHHHHHHH
Confidence 345788889899998884 23457899999999999997653
No 234
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=27.22 E-value=2.6e+02 Score=22.99 Aligned_cols=41 Identities=17% Similarity=0.132 Sum_probs=32.5
Q ss_pred hhchHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 169 RLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
-+.......+..||+.-+ -++...|+-||+.|..+-..|+.
T Consensus 51 ~l~~~Er~~i~~aL~~~~--gn~s~AAr~LGIsRsTL~rKLkr 91 (95)
T PRK00430 51 VLAEVEAPLLDMVMQYTR--GNQTRAALMLGINRGTLRKKLKK 91 (95)
T ss_pred HHHHHHHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHH
Confidence 355667778888998753 45889999999999998888775
No 235
>KOG2268 consensus Serine/threonine protein kinase [Signal transduction mechanisms; General function prediction only]
Probab=27.20 E-value=1.7e+02 Score=30.93 Aligned_cols=21 Identities=29% Similarity=0.360 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHhCCccccc
Q 040593 117 EDLDKLATELAEALGDVDMDM 137 (342)
Q Consensus 117 ed~a~~e~el~~a~gd~~~~~ 137 (342)
+|+-..++-+.+++|+.....
T Consensus 369 ~d~~e~~~~~~e~~~~~~en~ 389 (465)
T KOG2268|consen 369 EDAQEEEERIIEALGSGVENL 389 (465)
T ss_pred HHHHHHHHHHHHHHhcccccc
Confidence 566777788899999664443
No 236
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=27.18 E-value=1.1e+02 Score=24.96 Aligned_cols=32 Identities=31% Similarity=0.230 Sum_probs=26.0
Q ss_pred HHHHHHHhcCccccHHHHHHHhcCCHHHHHHH
Q 040593 177 KLAYALKTGRRKVSVKSLAAELCLDRAVVLEM 208 (342)
Q Consensus 177 rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~w 208 (342)
.+.-.+..+-+-+|=.+||.+||+.|+.|..-
T Consensus 8 ~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~ 39 (79)
T COG1654 8 LLLLLLLLTGNFVSGEKLAEELGISRTAVWKH 39 (79)
T ss_pred HHHHHHHcCCCcccHHHHHHHHCccHHHHHHH
Confidence 34456677788999999999999999998543
No 237
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=27.11 E-value=68 Score=29.28 Aligned_cols=25 Identities=12% Similarity=0.246 Sum_probs=22.3
Q ss_pred ccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 189 VSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
++|++||+++|+.++.|=--|.+.+
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~~ 26 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKTR 26 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC
Confidence 5899999999999999999997754
No 238
>cd03022 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK).
Probab=26.93 E-value=1e+02 Score=25.93 Aligned_cols=37 Identities=24% Similarity=0.237 Sum_probs=26.0
Q ss_pred HHHHHHHhcCccc----cHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 177 KLAYALKTGRRKV----SVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 177 rLarAL~~GRRKv----sIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
.|-+|+=.+.+.+ .|.++|.++|||.+.+.+++.++.
T Consensus 108 ~lf~a~~~~~~~i~~~~~l~~~a~~~Gld~~~~~~~~~~~~ 148 (192)
T cd03022 108 AVFRALWGEGLDIADPAVLAAVAAAAGLDADELLAAADDPA 148 (192)
T ss_pred HHHHHHhCCCCCCCCHHHHHHHHHHcCCCHHHHHHHcCCHH
Confidence 3444443333433 378899999999999999987765
No 239
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=26.85 E-value=78 Score=30.09 Aligned_cols=50 Identities=8% Similarity=0.040 Sum_probs=42.1
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCC
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPEC 327 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~ 327 (342)
..||..+.+.|.-++.- ....+||+.+|+++..|+.+.+|=+.|-++..+
T Consensus 189 ~~LT~RE~evl~l~a~G------~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr 238 (247)
T TIGR03020 189 GLITAREAEILAWVRDG------KTNEEIAAILGISSLTVKNHLQHIFKKLDVRNR 238 (247)
T ss_pred cCCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCH
Confidence 46999999999976532 445678999999999999999999999998764
No 240
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=26.44 E-value=45 Score=35.59 Aligned_cols=15 Identities=33% Similarity=0.282 Sum_probs=8.4
Q ss_pred HHHHHHhcCCHHHHH
Q 040593 192 KSLAAELCLDRAVVL 206 (342)
Q Consensus 192 k~LA~EL~LDRa~VL 206 (342)
=.||-.||=+=-++|
T Consensus 224 y~La~~l~r~~~d~L 238 (622)
T PF02724_consen 224 YELASSLGRDDNDLL 238 (622)
T ss_pred HHHHHHhCCCchHHH
Confidence 356766665544443
No 241
>PRK00215 LexA repressor; Validated
Probab=25.99 E-value=70 Score=28.24 Aligned_cols=46 Identities=15% Similarity=0.217 Sum_probs=35.9
Q ss_pred CCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCC-ChhhHHhhhhhhhhc
Q 040593 274 LKKVQVKTLEMVYR---RSKRPTDAMISSIVQVTNL-PRRRIVKWFEDKRAE 321 (342)
Q Consensus 274 FT~~QLetLErvF~---rT~YPdv~~RE~LA~~t~L-pesrVQVWFQNRRAK 321 (342)
+|..|.+.|+...+ ++.+| ....+||..+|+ +.+.|..+.+.=..+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~~L~~~ 51 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLKALERK 51 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 68899999998874 34443 346789999999 999999987765555
No 242
>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=25.87 E-value=1.6e+02 Score=21.54 Aligned_cols=35 Identities=31% Similarity=0.387 Sum_probs=25.1
Q ss_pred HHHHHHHHhcCcc----c-cHHHHHHHhcCCHHHHHHHhc
Q 040593 176 RKLAYALKTGRRK----V-SVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 176 ~rLarAL~~GRRK----v-sIk~LA~EL~LDRa~VL~wLR 210 (342)
..|..++..|+-+ . +...||+.+|+.|..|-+-|+
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~ 46 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALR 46 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHH
Confidence 4566777777754 5 899999999999999876553
No 243
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=25.82 E-value=79 Score=27.15 Aligned_cols=41 Identities=20% Similarity=0.279 Sum_probs=34.0
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhh
Q 040593 279 VKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 279 LetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
++.--..|...-|..+++ ++||+..|++...|-.+|.||-.
T Consensus 17 l~aa~~lf~~~G~~~~ti-~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 17 IETAIAQFALRGVSNTTL-NDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHHcCcccCCH-HHHHHHcCCCHHHHHHHcCCHHH
Confidence 455667788888877665 78999999999999999999865
No 244
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=25.66 E-value=1e+02 Score=21.33 Aligned_cols=23 Identities=26% Similarity=0.304 Sum_probs=20.5
Q ss_pred ccHHHHHHHhcCCHHHHHHHhcC
Q 040593 189 VSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.+++.+|+++|++=..|-.++..
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 79999999999999999887753
No 245
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=25.64 E-value=63 Score=23.54 Aligned_cols=25 Identities=4% Similarity=0.129 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCChhhHHhhhhhhhh
Q 040593 296 MISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 296 ~RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
...++|..+|++.+.|..|.++++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 5678999999999999999999885
No 246
>PF13309 HTH_22: HTH domain
Probab=25.17 E-value=72 Score=24.31 Aligned_cols=33 Identities=27% Similarity=0.301 Sum_probs=24.7
Q ss_pred HHHHHHhcC--ccccHHHHHHHhcCCHHHHHHHhc
Q 040593 178 LAYALKTGR--RKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 178 LarAL~~GR--RKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
+..-...|= =|=+|..+|+.||+.|..|-..||
T Consensus 30 V~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 30 VRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred HHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 333444553 345799999999999999988875
No 247
>PRK04217 hypothetical protein; Provisional
Probab=25.09 E-value=1.4e+02 Score=25.60 Aligned_cols=42 Identities=12% Similarity=0.136 Sum_probs=30.5
Q ss_pred hhhhchHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 167 EVRLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 167 ~~~L~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+..|..=|...+......|. ++++||+.||+.+..|-..|+.
T Consensus 40 ~~~Lt~eereai~l~~~eGl---S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL---TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC---CHHHHHHHHCcCHHHHHHHHHH
Confidence 34555555555544444554 9999999999999999888875
No 248
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.07 E-value=73 Score=26.78 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=35.0
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
..|+..|-..|+..|- .....+++|..+|+++..|.++++.-|.+
T Consensus 135 ~~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 135 QALPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREA 179 (187)
T ss_pred HhCCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4677888888877543 34567899999999999999999765554
No 249
>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=24.95 E-value=1.6e+02 Score=22.26 Aligned_cols=34 Identities=21% Similarity=0.179 Sum_probs=26.7
Q ss_pred HHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 177 KLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 177 rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
++-..+...-+++++..||+.|+++-..|-.||-
T Consensus 49 ~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~ 82 (105)
T PF01399_consen 49 RNLRQLSKPYSSISISEIAKALQLSEEEVESILI 82 (105)
T ss_dssp HHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHH
T ss_pred HHHHHHHHHhcccchHHHHHHhccchHHHHHHHH
Confidence 3344555599999999999999999988887764
No 250
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=24.90 E-value=2.1e+02 Score=22.99 Aligned_cols=25 Identities=12% Similarity=-0.124 Sum_probs=23.3
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
...+.+.||+.||+.++.|-.|.+.
T Consensus 77 ~gltq~~lA~~lg~~~~tis~~e~g 101 (127)
T TIGR03830 77 LGLSQREAAELLGGGVNAFSRYERG 101 (127)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4788999999999999999999998
No 251
>PRK11050 manganese transport regulator MntR; Provisional
Probab=24.72 E-value=1.3e+02 Score=26.06 Aligned_cols=36 Identities=19% Similarity=0.207 Sum_probs=28.8
Q ss_pred HHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 175 LRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 175 l~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+..|.+++..|- .+++++||..|++++..|-.+|+.
T Consensus 39 l~~I~~~l~~~~-~~t~~eLA~~l~is~stVsr~l~~ 74 (152)
T PRK11050 39 VELIADLIAEVG-EARQVDIAARLGVSQPTVAKMLKR 74 (152)
T ss_pred HHHHHHHHHhcC-CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 346667776642 578999999999999999998865
No 252
>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=24.71 E-value=68 Score=23.19 Aligned_cols=21 Identities=14% Similarity=0.422 Sum_probs=18.6
Q ss_pred HHHHHHHhCCChhhHHhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQN 317 (342)
..++|+.+|++.+.|..|-+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568999999999999999863
No 253
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=24.68 E-value=96 Score=39.10 Aligned_cols=82 Identities=27% Similarity=0.471 Sum_probs=0.0
Q ss_pred CCcCCCCCCCCCcHHHHHHHHHHHhhcC--CCCCCCCCCCCCCHHHHHHHHHHHHHHhCCccccccCCCC----------
Q 040593 75 PRKDIKDSDEEDDPFEALFSLLEEDLKN--DDSTIDDDDEEIDEEDLDKLATELAEALGDVDMDMSDTAT---------- 142 (342)
Q Consensus 75 ~~~~~~~~~~d~da~E~LF~~LEeDLkn--d~~s~~dddd~iseed~a~~e~el~~a~gd~~~~~~~~~~---------- 142 (342)
++.++-+|.++++|.| ||-|... .|+-+...|++-|||+ +++|-|-+.|+.-++.|+..
T Consensus 3844 ed~~~~~d~de~ea~e-----le~dm~g~~~ds~~~enen~dse~e----~qdldeevndi~ed~~nslneklwde~~~e 3914 (4600)
T COG5271 3844 EDTANQSDLDESEARE-----LESDMNGVTKDSVVSENENSDSEEE----NQDLDEEVNDIPEDLSNSLNEKLWDEPNEE 3914 (4600)
T ss_pred cccccccccchHHHHH-----hhhccccccccccccccCCCcchhh----hhhhhhhhhcCCcccchhhhHhhcCCcchh
Q ss_pred ---------------------CCCCCCCcccCCCCCCchhHhhh
Q 040593 143 ---------------------DGTESDNNEAHKEDGEDEEEEEE 165 (342)
Q Consensus 143 ---------------------~~~~~~~d~~~~~~~~~~~~~~e 165 (342)
...++||.+-|++|..+.+|++|
T Consensus 3915 d~~eteqk~~eqsa~nne~~~~~kedd~~a~ed~d~q~~~de~e 3958 (4600)
T COG5271 3915 DLLETEQKSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEE 3958 (4600)
T ss_pred hhhhhhhhhhhhhhhcchhhccccccCCCCccccchhhhcchhh
No 254
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.67 E-value=5e+02 Score=23.11 Aligned_cols=96 Identities=11% Similarity=0.082 Sum_probs=64.9
Q ss_pred CccccHHHHHHHhcCCHHHHHHHhcCCCCchhhhcccCCCCCCCcccccccCCCcccccccccccCCCCCCCCCCCcccc
Q 040593 186 RRKVSVKSLAAELCLDRAVVLEMLGDPPPNLLMLSATLPDKPTPTVLVNEVKHSEPIVAETTVHAVEPKSKVEEPVHDRQ 265 (342)
Q Consensus 186 RRKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~mSa~lpdE~~~~~~~~E~~~~~~v~~ets~~a~e~~~~~~lP~~~~q 265 (342)
..-.||+++|+.+|+-.+.|..|++..-..=..+ |. +
T Consensus 19 ~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l----------------------------------------~~---~ 55 (138)
T COG3415 19 GEGLSCREAAKRFGVSISTVYRWVRRYRETGLDL----------------------------------------PP---K 55 (138)
T ss_pred HcCccHHHHHHHhCccHHHHHHHHHHhccccccc----------------------------------------cC---c
Confidence 4458999999999999999999998653321111 11 1
Q ss_pred ccccccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChh--hHHhhhhhhhhccCC
Q 040593 266 HRWSAQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRR--RIVKWFEDKRAEEGV 324 (342)
Q Consensus 266 ~~w~kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~Lpes--rVQVWFQNRRAKd~v 324 (342)
+.+.+-..++..|++.|...-+.-.+=...+++.|....|+.=. .|-.|++--=-.++-
T Consensus 56 ~~~GrP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~~v~~~l~~~GlsykK 116 (138)
T COG3415 56 PRKGRPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHASAVRRLLHELGLSYKK 116 (138)
T ss_pred cCCCCCcccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHHHHHHHHHHcCCCcCC
Confidence 23444456788888888777666667777777888888887655 566666544333333
No 255
>PRK12423 LexA repressor; Provisional
Probab=24.64 E-value=1.3e+02 Score=27.11 Aligned_cols=36 Identities=14% Similarity=0.179 Sum_probs=28.5
Q ss_pred HHHHHHHHHhcCccccHHHHHHHhcC-CHHHHHHHhc
Q 040593 175 LRKLAYALKTGRRKVSVKSLAAELCL-DRAVVLEMLG 210 (342)
Q Consensus 175 l~rLarAL~~GRRKvsIk~LA~EL~L-DRa~VL~wLR 210 (342)
+..|..++..|.-.-++.+||+.||+ -|+.|=+.|+
T Consensus 12 l~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~ 48 (202)
T PRK12423 12 LAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQ 48 (202)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 45666778888888899999999996 8988855443
No 256
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=24.54 E-value=56 Score=34.86 Aligned_cols=19 Identities=16% Similarity=0.060 Sum_probs=10.2
Q ss_pred ccccHHHH-HHHhcCCHHHH
Q 040593 187 RKVSVKSL-AAELCLDRAVV 205 (342)
Q Consensus 187 RKvsIk~L-A~EL~LDRa~V 205 (342)
.|+++.-| .+=+||--..|
T Consensus 231 ~r~~~d~LW~AIvGlT~q~i 250 (622)
T PF02724_consen 231 GRDDNDLLWLAIVGLTDQYI 250 (622)
T ss_pred CCCchHHHHHHHHhhhHHhh
Confidence 34444443 45566666655
No 257
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=24.47 E-value=1.2e+02 Score=26.66 Aligned_cols=31 Identities=10% Similarity=0.098 Sum_probs=27.6
Q ss_pred HHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 182 LKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 182 L~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
...|=.+|+|.+||++.|+.++.+--.+++-
T Consensus 32 ~e~Gy~~~s~~dIA~~aGvs~gtiY~hF~sK 62 (212)
T PRK15008 32 SQFGFHGTRLEQIAELAGVSKTNLLYYFPSK 62 (212)
T ss_pred HHhCcccCCHHHHHHHhCcCHHHHHHHCCCH
Confidence 4689999999999999999999998887663
No 258
>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=24.42 E-value=68 Score=23.64 Aligned_cols=21 Identities=14% Similarity=0.392 Sum_probs=18.6
Q ss_pred HHHHHHHhCCChhhHHhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQN 317 (342)
..++|+.+|++.+.|.-|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568999999999999999764
No 259
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=24.41 E-value=44 Score=27.82 Aligned_cols=30 Identities=3% Similarity=0.200 Sum_probs=24.5
Q ss_pred hcCCCCHHHHHHHHHHhCCChhhHHhhhhh
Q 040593 288 RSKRPTDAMISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 288 rT~YPdv~~RE~LA~~t~LpesrVQVWFQN 317 (342)
.++|-..-..+.||..+|++++.++.+|+.
T Consensus 19 ~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 19 EDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred HHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344555567799999999999999999985
No 260
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=24.39 E-value=1.1e+02 Score=26.29 Aligned_cols=31 Identities=13% Similarity=0.158 Sum_probs=27.1
Q ss_pred HHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 181 ALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 181 AL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
-.+.|--.++|.+||++.|+.++.+...+.+
T Consensus 24 f~e~G~~~~t~~~Ia~~agvs~~tlY~~F~s 54 (215)
T PRK10668 24 FSQQGVSATSLADIAKAAGVTRGAIYWHFKN 54 (215)
T ss_pred HHHcCcccCCHHHHHHHhCCChHHHHHHCCC
Confidence 3478999999999999999999998877754
No 261
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=24.23 E-value=1.1e+02 Score=28.95 Aligned_cols=24 Identities=17% Similarity=0.185 Sum_probs=22.2
Q ss_pred cccHHHHHHHhcCCHHHHHHHhcC
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+++.++||+.||++++.|-.+|+.
T Consensus 21 ~IS~~eLA~~L~iS~~Tvsr~Lk~ 44 (217)
T PRK14165 21 KISSSEFANHTGTSSKTAARILKQ 44 (217)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 689999999999999999988875
No 262
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=24.11 E-value=80 Score=24.32 Aligned_cols=21 Identities=24% Similarity=0.314 Sum_probs=17.9
Q ss_pred cHHHHHHHhcCCHHHHHHHhcC
Q 040593 190 SVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 190 sIk~LA~EL~LDRa~VL~wLR~ 211 (342)
+...||+-||+.+.-|-.| +.
T Consensus 11 ~~~~lAkalGVs~~aVs~W-~~ 31 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW-GE 31 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH-HT
T ss_pred CHHHHHHHHCCCHHHHHHh-cC
Confidence 5789999999999999999 44
No 263
>PRK09954 putative kinase; Provisional
Probab=23.75 E-value=1.3e+02 Score=28.67 Aligned_cols=33 Identities=15% Similarity=0.180 Sum_probs=26.9
Q ss_pred HHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 177 KLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 177 rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
++-+.|+..- ++|.++||..|++.|..|-..|+
T Consensus 7 ~il~~l~~~~-~~s~~~la~~l~~s~~~v~~~i~ 39 (362)
T PRK09954 7 EILAILRRNP-LIQQNEIADILQISRSRVAAHIM 39 (362)
T ss_pred HHHHHHHHCC-CCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445555544 69999999999999999998887
No 264
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=23.70 E-value=3.5e+02 Score=28.66 Aligned_cols=43 Identities=21% Similarity=0.282 Sum_probs=33.8
Q ss_pred ccccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHh
Q 040593 270 AQKRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVK 313 (342)
Q Consensus 270 kRTrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQV 313 (342)
.=..|+.-+-..|...|.-... ...+.++|++.+|+++.||..
T Consensus 553 ~l~~L~~rE~~Vl~~r~g~~~~-~~~tl~ei~~~lgvs~eRVrQ 595 (619)
T PRK05658 553 VLASLTPREAKVLRMRFGIDMN-TDHTLEEVGKQFDVTRERIRQ 595 (619)
T ss_pred HHHcCCHHHHHHHHHhcCCCCC-CCccHHHHHHHhCCCHHHHHH
Confidence 3357899999999999975433 234689999999999999974
No 265
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=23.65 E-value=90 Score=27.79 Aligned_cols=31 Identities=10% Similarity=0.204 Sum_probs=25.5
Q ss_pred HHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 181 ALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 181 AL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
|...|...++++.||.+++++...|-..|..
T Consensus 18 A~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~ 48 (164)
T PRK10857 18 ALNSEAGPVPLADISERQGISLSYLEQLFSR 48 (164)
T ss_pred HhCCCCCcCcHHHHHHHHCcCHHHHHHHHHH
Confidence 4556777899999999999999987776654
No 266
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=23.63 E-value=1e+02 Score=26.46 Aligned_cols=51 Identities=18% Similarity=0.175 Sum_probs=43.6
Q ss_pred ccCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccCCCCCC
Q 040593 272 KRLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEGVPECR 328 (342)
Q Consensus 272 TrFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~vp~~R 328 (342)
..||+-+.+.|.-+.+ ...-.+||+.++++++.|..--+|=-.|-||.++.
T Consensus 149 ~~Lt~rE~evl~~~~~------G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~~~~ 199 (216)
T PRK10840 149 KRLSPKESEVLRLFAE------GFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDI 199 (216)
T ss_pred ccCCHHHHHHHHHHHC------CCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHH
Confidence 3599999999998873 44567889999999999999999999999987653
No 267
>cd08797 Death_NFkB1_p105 Death domain of the Nuclear Factor-KappaB1 precursor protein p105. Death Domain (DD) of the Nuclear Factor-KappaB1 (NF-kB1) precursor protein p105. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB1 (or p50) is produced from the processing of the precursor protein p105, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the classical (or canonical) NF-kB pathway. In the cytosol, p50 forms an inactive complex with RelA (or p65) and the Inhibitor of NF-kB (IkB). Activation is triggered by the phosphorylation and degradation of IkB, resulting in the active DNA-binding p50-RelA dimer to migrate to the nucleus. The classical pathway regulates the majority of genes activated by NF-kB including those encod
Probab=23.06 E-value=1.3e+02 Score=24.62 Aligned_cols=42 Identities=21% Similarity=0.257 Sum_probs=31.5
Q ss_pred HHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC-CCCchhhh
Q 040593 176 RKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD-PPPNLLML 219 (342)
Q Consensus 176 ~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~-ppP~ll~m 219 (342)
.+|...|..+.-+=+-..||..||||| .+.+++. |.|--.+|
T Consensus 3 qkLc~~Ld~p~~~g~Wr~LA~kL~l~~--l~~~f~~~pSPt~~LL 45 (76)
T cd08797 3 QQLYKLLESPDPDKNWETLAQKLGLGI--LNNAFRLSPSPSKTLL 45 (76)
T ss_pred hHHHHHhCCCCCCCCHHHHHHHHCchh--HHHHHhCCCCcHHHHH
Confidence 467788887765557999999999999 5666766 66754444
No 268
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=22.79 E-value=92 Score=28.20 Aligned_cols=25 Identities=8% Similarity=0.139 Sum_probs=22.6
Q ss_pred ccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 189 VSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
++||+||+++|+.++.|=--|.+.+
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~~ 25 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKA 25 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC
Confidence 3799999999999999999998865
No 269
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=22.65 E-value=79 Score=22.65 Aligned_cols=24 Identities=21% Similarity=0.238 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCChhhHHhhhhhhh
Q 040593 296 MISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 296 ~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
....+|..+|++.+.|..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 467899999999999999999976
No 270
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=22.36 E-value=1.3e+02 Score=27.92 Aligned_cols=33 Identities=27% Similarity=0.344 Sum_probs=26.2
Q ss_pred HHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 178 LAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 178 LarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
|-.+|+.+.+-.++.+||+.+||+|+.|--+|.
T Consensus 9 iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~ 41 (246)
T COG1414 9 ILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQ 41 (246)
T ss_pred HHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 345566666668899999999999999977663
No 271
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=22.24 E-value=1.4e+02 Score=30.89 Aligned_cols=40 Identities=15% Similarity=0.176 Sum_probs=32.1
Q ss_pred chHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 171 KNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 171 ~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
+..-...|.+||..+. ++.++|+.||+.|+.+..-||...
T Consensus 472 ~~~E~~~i~~~l~~~~---~~~~aA~~LGisr~tL~rkl~~~g 511 (520)
T PRK10820 472 SRFERSVLTRLYRNYP---STRKLAKRLGVSHTAIANKLREYG 511 (520)
T ss_pred HHHHHHHHHHHHHHCC---CHHHHHHHhCCCHHHHHHHHHHcC
Confidence 4445567888888775 677999999999999999988744
No 272
>PF03066 Nucleoplasmin: Nucleoplasmin; InterPro: IPR004301 The nucleophosmin/nucleoplasmin family of chaperones includes nucleophosmin, nucleoplasmin and nucleoplasmin-like proteins. They function as nuclear chaperones which are needed for the proper assembly of nucleosomes and the attainment of proper higher order chromatin structures [].; GO: 0003676 nucleic acid binding; PDB: 2P1B_E 1XB9_I 1XE0_C 1NLQ_A 2VTX_E 1K5J_D 1EJY_N 1EE5_B 3T30_J.
Probab=22.12 E-value=30 Score=30.71 Aligned_cols=8 Identities=75% Similarity=0.862 Sum_probs=0.0
Q ss_pred hHhhhhhh
Q 040593 161 EEEEEREV 168 (342)
Q Consensus 161 ~~~~er~~ 168 (342)
+++++.|+
T Consensus 138 ~~ee~~p~ 145 (149)
T PF03066_consen 138 EEEEESPV 145 (149)
T ss_dssp --------
T ss_pred cccccCCC
Confidence 33344443
No 273
>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=22.11 E-value=1.5e+02 Score=26.08 Aligned_cols=46 Identities=15% Similarity=0.228 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHh---hhcCCCCHHHHHHHHHHhCCC-hhhHHhhhhhhhhc
Q 040593 274 LKKVQVKTLEMVY---RRSKRPTDAMISSIVQVTNLP-RRRIVKWFEDKRAE 321 (342)
Q Consensus 274 FT~~QLetLErvF---~rT~YPdv~~RE~LA~~t~Lp-esrVQVWFQNRRAK 321 (342)
+|..|.+.|+... .++.|| ....+||+.+|++ .+.|....+-=+.+
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~--~~~~ela~~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYP--PSIREIARAVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCC--CcHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 7888988888877 456776 3467899999999 99888877654444
No 274
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=21.98 E-value=49 Score=26.47 Aligned_cols=33 Identities=27% Similarity=0.191 Sum_probs=28.4
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcCCCCchhhh
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGDPPPNLLML 219 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~ppP~ll~m 219 (342)
.+.|+-..|..||+|=..|..|++.+---+++|
T Consensus 12 ~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L 44 (65)
T PF05344_consen 12 QQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL 44 (65)
T ss_pred ccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence 357899999999999999999999887666665
No 275
>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=21.91 E-value=1.9e+02 Score=21.26 Aligned_cols=34 Identities=26% Similarity=0.401 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHh
Q 040593 174 QLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEML 209 (342)
Q Consensus 174 Ql~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wL 209 (342)
|++-|..-++ -+.+++++||..||+....|..-+
T Consensus 7 q~~Ll~~L~~--~~~~~~~ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 7 QLKLLELLLK--NKWITLKELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHH--HTSBBHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHc--CCCCcHHHHHHHHCCCHHHHHHHH
Confidence 5566666666 778899999999999998876544
No 276
>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=21.76 E-value=2.2e+02 Score=22.89 Aligned_cols=40 Identities=25% Similarity=0.367 Sum_probs=27.8
Q ss_pred hhchHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhc
Q 040593 169 RLKNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLG 210 (342)
Q Consensus 169 ~L~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR 210 (342)
.|..=|...|..-...| -+++++||..+|++++.|-..|+
T Consensus 25 ~lt~~q~~iL~~l~~~~--~~t~~ela~~~~~~~~tvs~~l~ 64 (118)
T TIGR02337 25 GLTEQQWRILRILAEQG--SMEFTQLANQACILRPSLTGILA 64 (118)
T ss_pred CCCHHHHHHHHHHHHcC--CcCHHHHHHHhCCCchhHHHHHH
Confidence 34444555565443444 48899999999999998876664
No 277
>PF04031 Las1: Las1-like ; InterPro: IPR007174 Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth [].
Probab=21.67 E-value=98 Score=27.46 Aligned_cols=23 Identities=35% Similarity=0.418 Sum_probs=20.1
Q ss_pred HhcCccccHHHHHHHhcCCHHHH
Q 040593 183 KTGRRKVSVKSLAAELCLDRAVV 205 (342)
Q Consensus 183 ~~GRRKvsIk~LA~EL~LDRa~V 205 (342)
..|....||..||+++||+.-+|
T Consensus 96 Q~~~~a~si~~~A~~iglP~~lV 118 (154)
T PF04031_consen 96 QQGKYARSIASLAKEIGLPSWLV 118 (154)
T ss_pred hccchhhhHHHHHHHcCCCHHHH
Confidence 34888999999999999998666
No 278
>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=21.54 E-value=87 Score=22.94 Aligned_cols=21 Identities=5% Similarity=0.232 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhhHHhhhhh
Q 040593 297 ISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 297 RE~LA~~t~LpesrVQVWFQN 317 (342)
..++|+.+|++.+.|+-|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568899999999999999765
No 279
>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=21.45 E-value=2.1e+02 Score=20.82 Aligned_cols=32 Identities=25% Similarity=0.324 Sum_probs=23.9
Q ss_pred HHHHHHHhcCccccHHHHHHHhcCCHHHHHHHh
Q 040593 177 KLAYALKTGRRKVSVKSLAAELCLDRAVVLEML 209 (342)
Q Consensus 177 rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wL 209 (342)
++-++| .+....+++.||++||+..+.|-.-|
T Consensus 14 ~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL 45 (61)
T PF12840_consen 14 RILRLL-ASNGPMTVSELAEELGISQSTVSYHL 45 (61)
T ss_dssp HHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 444555 56678899999999999999886544
No 280
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=21.43 E-value=1e+02 Score=24.15 Aligned_cols=25 Identities=16% Similarity=0.306 Sum_probs=20.9
Q ss_pred cCccccHHHHHHHhcCCHHHHHHHh
Q 040593 185 GRRKVSVKSLAAELCLDRAVVLEML 209 (342)
Q Consensus 185 GRRKvsIk~LA~EL~LDRa~VL~wL 209 (342)
.--++..++||.+||+.-..|=.|=
T Consensus 19 ~~g~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred hCCCccHHHHHHHHCCCHHHHHHHh
Confidence 3346789999999999999998874
No 281
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=21.21 E-value=37 Score=27.22 Aligned_cols=22 Identities=18% Similarity=0.279 Sum_probs=19.6
Q ss_pred HHHHHHHHHhCCChhhHHhhhh
Q 040593 295 AMISSIVQVTNLPRRRIVKWFE 316 (342)
Q Consensus 295 ~~RE~LA~~t~LpesrVQVWFQ 316 (342)
.+++.|...++|+..+|.|||+
T Consensus 54 ~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 54 ELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHHHhCCCCCeEEEEEE
Confidence 4678899999999999999986
No 282
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=21.07 E-value=80 Score=26.86 Aligned_cols=24 Identities=25% Similarity=0.437 Sum_probs=18.7
Q ss_pred cccHHHHHHHhcCCHHHHHHHhcC
Q 040593 188 KVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 188 KvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
..|+..||.++|..|+-|-++++-
T Consensus 33 DlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 33 DLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 579999999999999999999874
No 283
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=21.05 E-value=1e+02 Score=27.93 Aligned_cols=25 Identities=24% Similarity=0.344 Sum_probs=22.9
Q ss_pred ccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 189 VSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
++||++|++.|+..+.|=--|.+.+
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~ 26 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNP 26 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCC
Confidence 5899999999999999999998865
No 284
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=21.03 E-value=89 Score=33.02 Aligned_cols=8 Identities=25% Similarity=0.351 Sum_probs=3.1
Q ss_pred cccccccc
Q 040593 66 SSKKKKKS 73 (342)
Q Consensus 66 s~~k~k~~ 73 (342)
+-+|.|+.
T Consensus 20 ~~~~~KlT 27 (458)
T PF10446_consen 20 TDYKRKLT 27 (458)
T ss_pred cccccccc
Confidence 33444333
No 285
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=20.71 E-value=1.1e+02 Score=28.28 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=22.5
Q ss_pred ccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 189 VSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 189 vsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
++|+++|+..|+..+.|=--|.+.+
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~ 26 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVINNSP 26 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhCCCC
Confidence 6899999999999999999997754
No 286
>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=20.66 E-value=89 Score=25.99 Aligned_cols=21 Identities=14% Similarity=0.457 Sum_probs=19.5
Q ss_pred HHHHHHHHhCCChhhHHhhhh
Q 040593 296 MISSIVQVTNLPRRRIVKWFE 316 (342)
Q Consensus 296 ~RE~LA~~t~LpesrVQVWFQ 316 (342)
.+.++|...+++.+.|..||+
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHH
Confidence 567899999999999999999
No 287
>KOG0165 consensus Microtubule-associated protein Asp [Cytoskeleton]
Probab=20.65 E-value=1.9e+02 Score=32.99 Aligned_cols=47 Identities=32% Similarity=0.568 Sum_probs=35.6
Q ss_pred cHHHHHHHHHHHhhcC----CCCCCCCCCCCCCHH----HHHHHHHHHHHHhCCc
Q 040593 87 DPFEALFSLLEEDLKN----DDSTIDDDDEEIDEE----DLDKLATELAEALGDV 133 (342)
Q Consensus 87 da~E~LF~~LEeDLkn----d~~s~~dddd~isee----d~a~~e~el~~a~gd~ 133 (342)
.-+|.||-.|=+|.|| -.+++.=+||--++| ++.++++|++.++|.|
T Consensus 834 erlEmLfqslsedqknfvkTnnlsvsieDdantpelrrielkrkqqeIarklgnI 888 (1023)
T KOG0165|consen 834 ERLEMLFQSLSEDQKNFVKTNNLSVSIEDDANTPELRRIELKRKQQEIARKLGNI 888 (1023)
T ss_pred HHHHHHHHhhhHHHHHHHhhcccceeeccccCCHHHHHHHHHHHHHHHHHHhCCC
Confidence 4689999999999987 456654444433333 7888999999999987
No 288
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=20.63 E-value=1.2e+02 Score=25.73 Aligned_cols=33 Identities=21% Similarity=0.266 Sum_probs=28.7
Q ss_pred HHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 180 YALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 180 rAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
-..+.|=..|||.+||++.|+.|+.+-..+++-
T Consensus 20 lf~e~G~~~tSi~~Ia~~aGvsk~~lY~~F~sK 52 (192)
T PRK14996 20 VALAEGFAAMTVRRIASEAQVAAGQVHHHFSSA 52 (192)
T ss_pred HHHhcChhhccHHHHHHHhCCCcHHHHHHcCCH
Confidence 345689999999999999999999999988653
No 289
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.60 E-value=2.5e+02 Score=21.95 Aligned_cols=44 Identities=18% Similarity=0.271 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHhhh-----cCCCCHHHHHHHHHHhCCChhhHHhhhhh
Q 040593 274 LKKVQVKTLEMVYRR-----SKRPTDAMISSIVQVTNLPRRRIVKWFED 317 (342)
Q Consensus 274 FT~~QLetLErvF~r-----T~YPdv~~RE~LA~~t~LpesrVQVWFQN 317 (342)
+|..|+..|..+|.. +.+-+......+-...|+++..|..+|..
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~~ 52 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWNL 52 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 678899999999875 45677777777777789999999988863
No 290
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.57 E-value=80 Score=26.69 Aligned_cols=24 Identities=4% Similarity=-0.006 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCChhhHHhhhhhhh
Q 040593 296 MISSIVQVTNLPRRRIVKWFEDKR 319 (342)
Q Consensus 296 ~RE~LA~~t~LpesrVQVWFQNRR 319 (342)
.+++||+.+|++.+.|..|.++++
T Consensus 20 sq~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 20 TKKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 378899999999999999999985
No 291
>PRK00118 putative DNA-binding protein; Validated
Probab=20.54 E-value=1.2e+02 Score=25.72 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
.++..|-+.+...|.. .....+||+.+|+|+..|..|...-|.+
T Consensus 17 ~L~ekqRevl~L~y~e-----g~S~~EIAe~lGIS~~TV~r~L~RArkk 60 (104)
T PRK00118 17 LLTEKQRNYMELYYLD-----DYSLGEIAEEFNVSRQAVYDNIKRTEKL 60 (104)
T ss_pred cCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4566777777555443 4456789999999999999998755543
No 292
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=20.41 E-value=1.1e+02 Score=24.50 Aligned_cols=44 Identities=9% Similarity=0.042 Sum_probs=32.6
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhc
Q 040593 273 RLKKVQVKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAE 321 (342)
Q Consensus 273 rFT~~QLetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAK 321 (342)
.++..+-+.|...|- ......+||+.+|+|+..|..+...-|.+
T Consensus 113 ~L~~~~r~il~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-----EGKSYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred HCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 567777777777553 23346678999999999999998765554
No 293
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=20.33 E-value=1.4e+02 Score=24.87 Aligned_cols=45 Identities=7% Similarity=0.274 Sum_probs=31.7
Q ss_pred cccCCHHH-HHHHHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhh
Q 040593 271 QKRLKKVQ-VKTLEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRA 320 (342)
Q Consensus 271 RTrFT~~Q-LetLErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRA 320 (342)
|++||.+. ++.+..++.. ...+.++|..+|++...|-.|.+.=+.
T Consensus 10 rr~ys~EfK~~aV~~~~~~-----g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEP-----GMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCHHHHHHHHHHHHcC-----CCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 56677665 5555555552 234667899999999999999776443
No 294
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=20.31 E-value=1.9e+02 Score=29.01 Aligned_cols=40 Identities=23% Similarity=0.343 Sum_probs=33.4
Q ss_pred chHHHHHHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcC
Q 040593 171 KNWQLRKLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGD 211 (342)
Q Consensus 171 ~~WQl~rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~ 211 (342)
.=|. ++|.++|......+||++|++..|+...+|+.=|..
T Consensus 207 ~YW~-~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~ 246 (290)
T PLN03238 207 SYWT-RVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQS 246 (290)
T ss_pred HHHH-HHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHH
Confidence 3455 667788877677999999999999999999988874
No 295
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.31 E-value=2.2e+02 Score=24.05 Aligned_cols=34 Identities=12% Similarity=0.180 Sum_probs=27.7
Q ss_pred HHHHHHHhcCccccHHHHHHHhcCCHHHHHHHhcCC
Q 040593 177 KLAYALKTGRRKVSVKSLAAELCLDRAVVLEMLGDP 212 (342)
Q Consensus 177 rLarAL~~GRRKvsIk~LA~EL~LDRa~VL~wLR~p 212 (342)
+|.+.++ .+..+.++||+.+|+.++.+-.|.++.
T Consensus 9 ~l~~ll~--~~Glsq~eLA~~~Gis~~~is~iE~g~ 42 (120)
T PRK13890 9 NVLRLLD--ERHMTKKELSERSGVSISFLSDLTTGK 42 (120)
T ss_pred HHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 4444444 677899999999999999999999874
No 296
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=20.29 E-value=1.2e+02 Score=24.48 Aligned_cols=27 Identities=19% Similarity=0.134 Sum_probs=24.1
Q ss_pred ccccHHHHHHHhcCCHHHHHHHhcCCC
Q 040593 187 RKVSVKSLAAELCLDRAVVLEMLGDPP 213 (342)
Q Consensus 187 RKvsIk~LA~EL~LDRa~VL~wLR~pp 213 (342)
...|+++||++||+....|=.|++...
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~ 57 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGET 57 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCc
Confidence 467999999999999999999998743
No 297
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=20.28 E-value=1.4e+02 Score=23.87 Aligned_cols=52 Identities=12% Similarity=0.172 Sum_probs=38.9
Q ss_pred HHHHhhhcCCCCHHHHHHHHHHhCCChhhHHhhhhhhhhccC-CCCCCCccccCCC
Q 040593 282 LEMVYRRSKRPTDAMISSIVQVTNLPRRRIVKWFEDKRAEEG-VPECRKPFQRSDP 336 (342)
Q Consensus 282 LErvF~rT~YPdv~~RE~LA~~t~LpesrVQVWFQNRRAKd~-vp~~R~~~qrs~~ 336 (342)
++++.... +.....++|..+|+.+.+.-.|...+.--.+ ...+..|||+.+.
T Consensus 15 ~d~~~~~~---~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l~~~~~~~~~p~q~~~~ 67 (111)
T PF03374_consen 15 YDAFVDSD---GLYTIREAAKLLGIGRNKLFQWLREKGWLYRRGKGRNLPYQKYID 67 (111)
T ss_pred HHHHHcCC---CCccHHHHHHHhCCCHHHHHHHHHhCCceEECCCCCcccChhhhc
Confidence 34444444 5667788999999999999999998776666 5567788887543
No 298
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.26 E-value=92 Score=24.00 Aligned_cols=31 Identities=23% Similarity=0.519 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChhhHHhhhhhhhhcc--CCCC
Q 040593 296 MISSIVQVTNLPRRRIVKWFEDKRAEE--GVPE 326 (342)
Q Consensus 296 ~RE~LA~~t~LpesrVQVWFQNRRAKd--~vp~ 326 (342)
...++|+.+|++++.|..|.++=+..- ++.+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~ 46 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLP 46 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHh
Confidence 478899999999999999999866553 4444
Done!