Query 041877
Match_columns 254
No_of_seqs 272 out of 1386
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 11:38:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041877hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.9 1E-22 2.3E-27 177.3 13.3 103 33-135 49-151 (198)
2 KOG0489 Transcription factor z 99.7 1.6E-18 3.5E-23 157.1 4.8 62 32-93 157-218 (261)
3 KOG0842 Transcription factor t 99.7 4.1E-18 8.8E-23 156.8 6.2 58 41-98 160-217 (307)
4 KOG0488 Transcription factor B 99.7 3.7E-17 7.9E-22 151.5 7.4 62 32-93 170-231 (309)
5 KOG0487 Transcription factor A 99.7 1.2E-17 2.7E-22 153.6 3.7 64 32-95 233-296 (308)
6 KOG0843 Transcription factor E 99.7 1.1E-16 2.4E-21 136.5 6.0 64 33-96 101-164 (197)
7 KOG0484 Transcription factor P 99.7 1.1E-16 2.3E-21 125.9 5.4 63 31-93 14-76 (125)
8 KOG0485 Transcription factor N 99.6 2.9E-16 6.2E-21 137.6 6.9 59 35-93 105-163 (268)
9 PF00046 Homeobox: Homeobox do 99.6 5.7E-16 1.2E-20 108.5 6.5 57 35-91 1-57 (57)
10 KOG0850 Transcription factor D 99.6 5.1E-16 1.1E-20 136.9 7.3 68 25-92 113-180 (245)
11 KOG2251 Homeobox transcription 99.6 4.5E-16 9.8E-21 136.5 5.1 65 29-93 32-96 (228)
12 KOG0848 Transcription factor C 99.6 1.3E-15 2.7E-20 136.9 4.4 53 41-93 206-258 (317)
13 KOG0492 Transcription factor M 99.6 3.1E-15 6.6E-20 130.3 6.4 59 35-93 145-203 (246)
14 KOG4577 Transcription factor L 99.6 1.3E-14 2.9E-19 131.7 9.0 89 31-120 164-252 (383)
15 KOG0494 Transcription factor C 99.5 1.2E-14 2.5E-19 130.4 7.9 57 38-94 145-201 (332)
16 cd00086 homeodomain Homeodomai 99.5 4.6E-14 9.9E-19 98.6 6.6 57 36-92 2-58 (59)
17 smart00389 HOX Homeodomain. DN 99.5 5.1E-14 1.1E-18 97.8 6.0 55 36-90 2-56 (56)
18 COG5576 Homeodomain-containing 99.5 5.1E-14 1.1E-18 118.9 6.3 64 30-93 47-110 (156)
19 KOG0493 Transcription factor E 99.4 5.9E-14 1.3E-18 126.0 3.7 64 38-101 250-313 (342)
20 TIGR01565 homeo_ZF_HD homeobox 99.4 1.6E-13 3.4E-18 97.9 4.9 52 35-86 2-57 (58)
21 KOG0844 Transcription factor E 99.4 7.3E-14 1.6E-18 127.7 3.5 65 31-95 178-242 (408)
22 KOG0486 Transcription factor P 99.4 1.2E-13 2.7E-18 126.5 4.3 62 33-94 111-172 (351)
23 KOG0491 Transcription factor B 99.3 3.2E-13 6.9E-18 114.1 2.4 59 35-93 101-159 (194)
24 KOG3802 Transcription factor O 99.3 6.8E-13 1.5E-17 125.1 3.2 61 33-93 293-353 (398)
25 KOG0847 Transcription factor, 99.3 2.4E-12 5.2E-17 113.3 4.3 63 31-93 164-226 (288)
26 KOG0490 Transcription factor, 99.1 1.7E-11 3.7E-16 107.1 3.0 62 32-93 58-119 (235)
27 KOG0849 Transcription factor P 99.0 7.6E-10 1.6E-14 104.6 6.0 62 32-93 174-235 (354)
28 KOG1168 Transcription factor A 98.9 3E-10 6.5E-15 103.6 2.3 64 30-93 305-368 (385)
29 KOG0775 Transcription factor S 98.7 2.3E-08 5.1E-13 90.7 4.7 51 41-91 183-233 (304)
30 KOG0774 Transcription factor P 98.5 7.3E-08 1.6E-12 87.1 2.8 59 34-92 188-249 (334)
31 PF05920 Homeobox_KN: Homeobox 98.3 5.4E-07 1.2E-11 59.7 3.3 34 55-88 7-40 (40)
32 KOG0490 Transcription factor, 97.9 1.3E-05 2.8E-10 69.9 5.1 62 32-93 151-212 (235)
33 KOG2252 CCAAT displacement pro 97.8 3.1E-05 6.6E-10 76.4 6.1 60 30-89 416-475 (558)
34 PF02183 HALZ: Homeobox associ 97.4 0.00031 6.8E-09 47.7 5.0 42 92-133 1-42 (45)
35 KOG1146 Homeobox protein [Gene 97.2 0.0006 1.3E-08 73.1 6.0 66 29-94 898-963 (1406)
36 PF11569 Homez: Homeodomain le 96.7 0.0015 3.2E-08 46.4 2.6 42 46-87 10-51 (56)
37 KOG0773 Transcription factor M 96.5 0.0027 5.8E-08 59.5 4.3 58 36-93 241-301 (342)
38 KOG3623 Homeobox transcription 94.0 0.075 1.6E-06 54.7 4.9 48 46-93 568-615 (1007)
39 PF04218 CENP-B_N: CENP-B N-te 93.9 0.14 3.1E-06 35.5 4.8 47 35-86 1-47 (53)
40 PRK09413 IS2 repressor TnpA; R 93.8 0.85 1.8E-05 36.6 9.8 44 36-84 8-52 (121)
41 smart00340 HALZ homeobox assoc 89.2 0.93 2E-05 30.4 4.3 32 93-124 2-33 (44)
42 KOG4005 Transcription factor X 89.1 4.7 0.0001 36.7 10.2 33 96-128 97-129 (292)
43 KOG4196 bZIP transcription fac 82.6 27 0.00058 29.0 11.2 77 39-128 22-113 (135)
44 PF02183 HALZ: Homeobox associ 82.4 4.3 9.2E-05 27.5 5.0 33 94-126 10-42 (45)
45 PRK00888 ftsB cell division pr 80.8 4.7 0.0001 31.9 5.5 46 76-122 15-60 (105)
46 PF01527 HTH_Tnp_1: Transposas 80.3 0.85 1.8E-05 32.8 1.1 46 36-85 2-47 (76)
47 PF04545 Sigma70_r4: Sigma-70, 78.6 6.3 0.00014 26.2 4.9 40 40-84 4-43 (50)
48 PF06005 DUF904: Protein of un 77.1 12 0.00025 27.8 6.3 36 95-130 17-52 (72)
49 PF00170 bZIP_1: bZIP transcri 74.9 18 0.00039 25.6 6.7 37 95-131 25-61 (64)
50 PF13443 HTH_26: Cro/C1-type H 74.2 4.6 0.0001 27.8 3.4 42 63-104 12-53 (63)
51 cd06171 Sigma70_r4 Sigma70, re 73.7 5.3 0.00011 25.5 3.4 43 40-87 10-52 (55)
52 PF04967 HTH_10: HTH DNA bindi 72.6 6.2 0.00013 27.6 3.7 40 41-80 1-42 (53)
53 PRK13169 DNA replication intia 71.3 13 0.00029 29.8 5.8 38 92-129 18-55 (110)
54 PF06156 DUF972: Protein of un 70.2 15 0.00032 29.3 5.8 40 92-131 18-57 (107)
55 smart00338 BRLZ basic region l 69.7 36 0.00079 24.0 7.5 38 95-132 25-62 (65)
56 KOG4571 Activating transcripti 67.8 18 0.00039 33.8 6.6 41 92-132 244-284 (294)
57 cd00569 HTH_Hin_like Helix-tur 67.2 18 0.00039 20.3 4.6 39 39-82 4-42 (42)
58 KOG3119 Basic region leucine z 66.8 15 0.00032 33.7 5.9 34 99-132 218-251 (269)
59 PF00170 bZIP_1: bZIP transcri 66.0 38 0.00083 23.8 6.8 39 88-126 25-63 (64)
60 PF06005 DUF904: Protein of un 62.1 44 0.00096 24.7 6.6 43 88-130 17-59 (72)
61 PF10668 Phage_terminase: Phag 61.4 6.4 0.00014 28.3 1.9 19 63-81 24-42 (60)
62 PF09607 BrkDBD: Brinker DNA-b 61.1 17 0.00036 26.1 4.0 44 38-83 3-47 (58)
63 PRK03975 tfx putative transcri 60.3 49 0.0011 27.6 7.4 48 38-91 4-51 (141)
64 PF07716 bZIP_2: Basic region 56.5 61 0.0013 22.1 6.2 26 98-123 27-52 (54)
65 PF10224 DUF2205: Predicted co 55.9 65 0.0014 24.5 6.7 37 93-129 27-63 (80)
66 PF13936 HTH_38: Helix-turn-he 55.3 16 0.00035 24.0 3.0 40 39-83 3-42 (44)
67 PF08281 Sigma70_r4_2: Sigma-7 50.9 42 0.00092 22.3 4.6 41 41-86 11-51 (54)
68 smart00338 BRLZ basic region l 50.5 76 0.0016 22.3 6.1 37 90-126 27-63 (65)
69 COG4467 Regulator of replicati 47.5 48 0.001 26.7 5.0 35 93-127 19-53 (114)
70 PF00196 GerE: Bacterial regul 46.3 52 0.0011 22.4 4.6 45 40-90 3-47 (58)
71 COG3413 Predicted DNA binding 46.2 38 0.00082 29.5 4.8 39 40-78 155-195 (215)
72 KOG4343 bZIP transcription fac 46.0 74 0.0016 32.4 7.1 33 99-131 305-337 (655)
73 COG2919 Septum formation initi 45.1 85 0.0019 25.1 6.3 37 96-132 50-86 (117)
74 PF15058 Speriolin_N: Sperioli 44.9 1.5E+02 0.0033 26.2 8.2 35 97-132 6-40 (200)
75 PRK04217 hypothetical protein; 44.3 68 0.0015 25.7 5.5 44 40-88 42-85 (110)
76 smart00421 HTH_LUXR helix_turn 43.8 85 0.0018 20.0 5.2 40 40-85 3-42 (58)
77 cd04761 HTH_MerR-SF Helix-Turn 43.8 21 0.00046 23.0 2.2 22 64-85 3-24 (49)
78 PF01166 TSC22: TSC-22/dip/bun 43.3 38 0.00082 24.3 3.4 29 96-124 14-42 (59)
79 PRK15422 septal ring assembly 43.2 1E+02 0.0022 23.4 5.9 24 95-118 17-40 (79)
80 PRK10072 putative transcriptio 42.8 41 0.0009 26.2 4.0 41 40-87 32-72 (96)
81 PF04977 DivIC: Septum formati 41.8 79 0.0017 22.5 5.2 30 93-122 21-50 (80)
82 TIGR02937 sigma70-ECF RNA poly 41.8 66 0.0014 24.6 5.1 45 41-90 111-155 (158)
83 TIGR02449 conserved hypothetic 41.3 89 0.0019 22.8 5.2 31 98-128 9-39 (65)
84 PF10224 DUF2205: Predicted co 41.2 1.6E+02 0.0034 22.4 6.8 44 88-131 15-58 (80)
85 PRK06759 RNA polymerase factor 41.0 75 0.0016 25.3 5.5 44 41-89 107-150 (154)
86 cd04765 HTH_MlrA-like_sg2 Heli 40.3 1.5E+02 0.0032 22.8 6.8 39 37-87 35-73 (99)
87 KOG3755 SATB1 matrix attachmen 40.0 14 0.00031 37.8 1.2 46 48-93 706-758 (769)
88 PF07407 Seadorna_VP6: Seadorn 39.6 32 0.0007 32.9 3.4 26 100-125 36-61 (420)
89 TIGR03879 near_KaiC_dom probab 39.3 14 0.0003 27.6 0.8 35 50-84 21-55 (73)
90 PF00424 REV: REV protein (ant 39.2 43 0.00092 26.1 3.5 34 46-93 14-47 (91)
91 KOG0249 LAR-interacting protei 39.1 1.8E+02 0.0038 30.9 8.7 45 87-131 214-258 (916)
92 PRK11924 RNA polymerase sigma 39.0 46 0.001 26.9 4.0 45 41-90 126-170 (179)
93 PRK09652 RNA polymerase sigma 39.0 47 0.001 26.9 4.0 45 41-90 129-173 (182)
94 PRK09646 RNA polymerase sigma 38.9 63 0.0014 27.2 4.9 46 41-91 143-188 (194)
95 PF02796 HTH_7: Helix-turn-hel 37.4 50 0.0011 21.6 3.2 39 39-82 4-42 (45)
96 PRK12514 RNA polymerase sigma 37.2 50 0.0011 27.2 4.0 46 41-91 130-175 (179)
97 KOG0150 Spliceosomal protein F 37.1 86 0.0019 29.7 5.7 49 78-126 16-65 (336)
98 PF08172 CASP_C: CASP C termin 36.9 1.3E+02 0.0028 27.4 6.8 45 86-130 90-134 (248)
99 KOG4005 Transcription factor X 36.9 1.5E+02 0.0033 27.2 7.1 32 94-125 102-133 (292)
100 PF08961 DUF1875: Domain of un 36.8 11 0.00025 33.9 0.0 35 95-129 128-162 (243)
101 PRK14127 cell division protein 36.7 77 0.0017 25.4 4.7 37 97-133 31-67 (109)
102 PF13518 HTH_28: Helix-turn-he 36.7 38 0.00083 22.0 2.6 22 63-84 14-35 (52)
103 smart00340 HALZ homeobox assoc 36.3 72 0.0016 21.5 3.7 31 103-133 5-35 (44)
104 KOG4343 bZIP transcription fac 35.4 66 0.0014 32.8 5.0 48 88-135 301-348 (655)
105 KOG1146 Homeobox protein [Gene 35.1 78 0.0017 35.5 5.8 56 38-93 709-764 (1406)
106 PRK00888 ftsB cell division pr 34.7 1.1E+02 0.0024 24.1 5.3 36 96-131 27-62 (105)
107 PF06056 Terminase_5: Putative 34.7 31 0.00067 24.3 2.0 26 64-91 16-41 (58)
108 PF08280 HTH_Mga: M protein tr 34.7 45 0.00097 23.2 2.8 34 44-81 6-39 (59)
109 PF11594 Med28: Mediator compl 34.7 1.6E+02 0.0034 23.6 6.1 35 75-112 17-51 (106)
110 KOG3623 Homeobox transcription 34.5 7.8 0.00017 40.6 -1.6 57 38-94 630-686 (1007)
111 COG2963 Transposase and inacti 34.4 2.1E+02 0.0045 22.1 6.9 43 38-84 5-48 (116)
112 PF06156 DUF972: Protein of un 34.4 1.5E+02 0.0032 23.6 6.0 44 92-135 11-54 (107)
113 PF13384 HTH_23: Homeodomain-l 34.0 33 0.00072 22.4 1.9 22 62-83 18-39 (50)
114 COG4367 Uncharacterized protei 33.9 56 0.0012 25.5 3.3 39 41-79 3-41 (97)
115 cd01392 HTH_LacI Helix-turn-he 33.5 44 0.00095 21.8 2.5 21 66-86 2-22 (52)
116 PRK12519 RNA polymerase sigma 33.4 56 0.0012 27.3 3.7 31 61-91 157-187 (194)
117 PRK09639 RNA polymerase sigma 33.3 1.3E+02 0.0028 24.1 5.8 44 41-90 113-156 (166)
118 PRK00118 putative DNA-binding 33.3 2.4E+02 0.0053 22.2 7.7 47 40-91 17-63 (104)
119 TIGR02985 Sig70_bacteroi1 RNA 33.1 68 0.0015 25.3 4.0 45 41-90 114-158 (161)
120 cd01106 HTH_TipAL-Mta Helix-Tu 32.7 2.2E+02 0.0048 21.6 8.4 37 37-86 35-71 (103)
121 PF13411 MerR_1: MerR HTH fami 32.1 38 0.00083 23.5 2.1 21 64-84 3-23 (69)
122 cd04770 HTH_HMRTR Helix-Turn-H 31.6 2.5E+02 0.0055 21.9 9.5 38 37-87 35-72 (123)
123 TIGR02948 SigW_bacill RNA poly 31.1 73 0.0016 26.2 4.0 46 41-91 137-182 (187)
124 PRK12526 RNA polymerase sigma 30.9 1.2E+02 0.0026 25.8 5.5 28 63-90 171-198 (206)
125 PRK10884 SH3 domain-containing 30.9 1.7E+02 0.0038 25.8 6.5 30 101-130 137-166 (206)
126 KOG2391 Vacuolar sorting prote 30.5 1.6E+02 0.0035 28.3 6.5 47 85-131 221-267 (365)
127 TIGR02209 ftsL_broad cell divi 30.5 1.7E+02 0.0037 21.3 5.5 30 93-122 28-57 (85)
128 PF05377 FlaC_arch: Flagella a 30.5 2E+02 0.0043 20.4 5.6 33 94-126 5-37 (55)
129 PRK10884 SH3 domain-containing 30.4 1.6E+02 0.0035 26.0 6.2 34 97-130 126-159 (206)
130 PF04977 DivIC: Septum formati 30.3 1.6E+02 0.0034 20.9 5.2 33 97-129 18-50 (80)
131 PF01381 HTH_3: Helix-turn-hel 30.3 39 0.00085 22.3 1.8 23 64-86 12-34 (55)
132 PRK09642 RNA polymerase sigma 30.1 59 0.0013 26.2 3.2 28 64-91 125-152 (160)
133 TIGR02209 ftsL_broad cell divi 30.1 1.7E+02 0.0038 21.2 5.5 39 78-116 20-58 (85)
134 cd04762 HTH_MerR-trunc Helix-T 29.8 50 0.0011 20.6 2.2 24 64-87 3-26 (49)
135 KOG4797 Transcriptional regula 29.8 1.1E+02 0.0025 24.7 4.6 30 95-124 66-95 (123)
136 cd06170 LuxR_C_like C-terminal 29.6 1.5E+02 0.0032 19.0 4.6 36 42-83 2-37 (57)
137 COG4026 Uncharacterized protei 29.4 1.8E+02 0.0039 26.6 6.3 17 101-117 140-156 (290)
138 PRK13729 conjugal transfer pil 29.3 1.3E+02 0.0029 30.1 6.0 44 90-133 77-120 (475)
139 PF13551 HTH_29: Winged helix- 29.2 1.6E+02 0.0035 21.9 5.4 44 40-83 57-109 (112)
140 PRK09648 RNA polymerase sigma 28.8 1.2E+02 0.0025 25.2 4.9 44 41-89 140-183 (189)
141 PRK12512 RNA polymerase sigma 28.6 98 0.0021 25.5 4.4 46 41-91 132-177 (184)
142 PF07407 Seadorna_VP6: Seadorn 28.5 91 0.002 30.0 4.4 19 97-115 40-58 (420)
143 TIGR02989 Sig-70_gvs1 RNA poly 28.0 1.5E+02 0.0032 23.6 5.2 43 41-88 112-154 (159)
144 cd04763 HTH_MlrA-like Helix-Tu 27.9 45 0.00098 23.4 1.9 21 64-84 3-23 (68)
145 cd04783 HTH_MerR1 Helix-Turn-H 27.7 3.1E+02 0.0067 21.7 8.8 37 37-86 35-71 (126)
146 PF00376 MerR: MerR family reg 27.6 46 0.001 21.3 1.7 18 65-82 3-20 (38)
147 PRK05602 RNA polymerase sigma 27.5 87 0.0019 26.0 3.9 28 63-90 146-173 (186)
148 TIGR02983 SigE-fam_strep RNA p 27.3 1.6E+02 0.0036 23.5 5.4 46 41-91 111-156 (162)
149 cd04764 HTH_MlrA-like_sg1 Heli 27.2 49 0.0011 23.1 1.9 21 64-84 3-23 (67)
150 cd00093 HTH_XRE Helix-turn-hel 27.0 52 0.0011 20.2 1.9 23 64-86 15-37 (58)
151 PRK13169 DNA replication intia 26.9 2.4E+02 0.0051 22.6 6.0 43 92-134 11-53 (110)
152 TIGR02051 MerR Hg(II)-responsi 26.9 3.2E+02 0.007 21.6 9.2 37 37-86 34-70 (124)
153 TIGR02894 DNA_bind_RsfA transc 26.5 1.8E+02 0.0039 25.0 5.5 56 73-128 80-136 (161)
154 PRK06986 fliA flagellar biosyn 26.5 1E+02 0.0022 26.9 4.3 46 41-91 185-230 (236)
155 PRK09047 RNA polymerase factor 26.3 2E+02 0.0044 22.8 5.8 43 41-88 107-149 (161)
156 TIGR02479 FliA_WhiG RNA polyme 25.3 1.1E+02 0.0025 26.3 4.3 45 41-90 176-220 (224)
157 TIGR03752 conj_TIGR03752 integ 25.0 1.4E+02 0.0031 29.8 5.4 28 40-70 41-68 (472)
158 TIGR02959 SigZ RNA polymerase 24.9 1.8E+02 0.004 23.8 5.4 39 41-84 101-139 (170)
159 PF07334 IFP_35_N: Interferon- 24.9 1.2E+02 0.0026 22.9 3.7 27 106-132 3-29 (76)
160 PRK05657 RNA polymerase sigma 24.8 1.4E+02 0.0031 27.8 5.2 50 40-90 262-311 (325)
161 PRK08301 sporulation sigma fac 24.8 1.5E+02 0.0032 25.8 5.0 49 41-90 179-227 (234)
162 cd04787 HTH_HMRTR_unk Helix-Tu 24.7 3.7E+02 0.008 21.5 8.8 73 37-124 35-107 (133)
163 PRK13922 rod shape-determining 24.7 1.5E+02 0.0033 26.6 5.2 16 95-110 75-90 (276)
164 PRK06811 RNA polymerase factor 24.7 1.3E+02 0.0028 25.1 4.4 46 41-91 132-177 (189)
165 TIGR02999 Sig-70_X6 RNA polyme 24.5 2E+02 0.0042 23.6 5.5 27 64-90 153-179 (183)
166 PRK12515 RNA polymerase sigma 24.3 2.3E+02 0.0049 23.5 5.9 46 41-91 132-177 (189)
167 smart00027 EH Eps15 homology d 24.1 1.8E+02 0.004 21.6 4.8 43 41-83 4-51 (96)
168 PRK10403 transcriptional regul 24.1 1.2E+02 0.0025 24.5 4.0 45 40-90 153-197 (215)
169 TIGR03070 couple_hipB transcri 24.1 59 0.0013 21.2 1.8 23 64-86 18-40 (58)
170 cd04779 HTH_MerR-like_sg4 Heli 24.1 4E+02 0.0087 21.7 9.7 66 37-115 34-100 (134)
171 PRK08295 RNA polymerase factor 23.9 2.1E+02 0.0045 23.9 5.7 30 61-90 170-199 (208)
172 PF09744 Jnk-SapK_ap_N: JNK_SA 23.9 4.5E+02 0.0098 22.3 8.2 72 45-123 34-109 (158)
173 PRK09644 RNA polymerase sigma 23.7 1.1E+02 0.0023 24.9 3.7 29 63-91 126-154 (165)
174 PF04999 FtsL: Cell division p 23.5 2.2E+02 0.0047 21.5 5.1 22 98-119 44-65 (97)
175 PRK14127 cell division protein 23.3 3.3E+02 0.0072 21.8 6.2 51 72-131 22-72 (109)
176 cd01104 HTH_MlrA-CarA Helix-Tu 23.0 72 0.0016 22.0 2.2 20 64-83 3-22 (68)
177 PRK12518 RNA polymerase sigma 22.7 96 0.0021 25.3 3.2 33 59-91 134-166 (175)
178 TIGR00721 tfx DNA-binding prot 22.7 4.5E+02 0.0097 21.8 7.3 46 39-90 5-50 (137)
179 PRK08583 RNA polymerase sigma 22.3 1.4E+02 0.003 26.4 4.4 45 41-90 206-250 (257)
180 PRK12530 RNA polymerase sigma 22.3 1.3E+02 0.0028 25.3 4.0 46 41-91 135-180 (189)
181 PRK09480 slmA division inhibit 22.2 1.1E+02 0.0023 25.2 3.4 40 47-87 17-56 (194)
182 PF03234 CDC37_N: Cdc37 N term 22.1 3.2E+02 0.0069 23.7 6.4 45 88-132 31-75 (177)
183 PRK13890 conjugal transfer pro 22.0 93 0.002 24.9 2.9 44 63-107 20-63 (120)
184 TIGR02954 Sig70_famx3 RNA poly 21.9 1.8E+02 0.0039 23.6 4.7 45 41-90 120-164 (169)
185 PRK10360 DNA-binding transcrip 21.9 1.4E+02 0.0031 23.9 4.1 44 40-89 137-180 (196)
186 TIGR02393 RpoD_Cterm RNA polym 21.6 2.3E+02 0.0051 24.7 5.7 51 40-91 176-226 (238)
187 TIGR02939 RpoE_Sigma70 RNA pol 21.6 1E+02 0.0022 25.3 3.2 30 61-90 154-183 (190)
188 PRK13919 putative RNA polymera 21.6 1.4E+02 0.0031 24.5 4.1 43 41-88 136-178 (186)
189 TIGR02950 SigM_subfam RNA poly 21.5 1E+02 0.0022 24.4 3.1 33 58-90 118-150 (154)
190 COG2919 Septum formation initi 21.4 2.6E+02 0.0057 22.2 5.4 50 75-125 37-86 (117)
191 PRK15369 two component system 21.3 3.1E+02 0.0068 21.6 6.0 45 40-90 149-193 (211)
192 PF00038 Filament: Intermediat 21.3 4.8E+02 0.01 23.6 7.8 55 75-129 186-249 (312)
193 PRK11511 DNA-binding transcrip 21.2 1.3E+02 0.0028 23.9 3.6 25 60-84 24-48 (127)
194 TIGR02952 Sig70_famx2 RNA poly 21.2 2E+02 0.0044 23.0 4.9 38 41-83 123-160 (170)
195 PRK13922 rod shape-determining 21.1 2.2E+02 0.0047 25.7 5.4 38 96-133 69-109 (276)
196 cd01109 HTH_YyaN Helix-Turn-He 21.1 3.9E+02 0.0086 20.6 9.7 37 37-86 35-71 (113)
197 PRK12538 RNA polymerase sigma 21.0 2.6E+02 0.0057 24.6 5.9 29 63-91 189-217 (233)
198 PRK12537 RNA polymerase sigma 20.8 2.5E+02 0.0054 23.2 5.4 44 41-89 134-177 (182)
199 PRK07037 extracytoplasmic-func 20.7 2.7E+02 0.0059 22.2 5.5 45 41-90 110-154 (163)
200 KOG0977 Nuclear envelope prote 20.5 3.6E+02 0.0078 27.6 7.2 41 91-131 150-190 (546)
201 cd00131 PAX Paired Box domain 20.5 4.2E+02 0.009 21.3 6.5 44 40-84 75-126 (128)
202 TIGR02941 Sigma_B RNA polymera 20.5 2.2E+02 0.0049 25.0 5.3 45 41-90 206-250 (255)
203 PF05529 Bap31: B-cell recepto 20.4 2.3E+02 0.0049 24.2 5.2 6 55-60 102-107 (192)
204 PF14662 CCDC155: Coiled-coil 20.3 3.5E+02 0.0075 23.9 6.2 38 85-122 84-121 (193)
205 TIGR01069 mutS2 MutS2 family p 20.2 4.2E+02 0.0091 28.0 8.0 21 59-79 480-500 (771)
206 KOG0709 CREB/ATF family transc 20.2 1.4E+02 0.003 29.9 4.1 13 40-52 220-232 (472)
207 COG4467 Regulator of replicati 20.1 3.8E+02 0.0082 21.7 5.9 44 92-135 11-54 (114)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.89 E-value=1e-22 Score=177.35 Aligned_cols=103 Identities=64% Similarity=0.931 Sum_probs=97.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 041877 33 QVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDYEVLKKQFEALKADN 112 (254)
Q Consensus 33 ~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~~~~~~lk~~~~~l~~e~ 112 (254)
...++|+||+.+|+..||+.|+...|+.+.+|..||++|||.+|||+|||||||||||.++++.+++.+|.+++.++.++
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~ 128 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEN 128 (198)
T ss_pred ccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhh
Confidence 35678889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhccCCC
Q 041877 113 DSLQAQNKKLHAELVSLKNKDSN 135 (254)
Q Consensus 113 ~~l~~e~~~l~~e~~~lk~~~~~ 135 (254)
..|+.++..|.+++..++.....
T Consensus 129 ~~Lq~e~~eL~~~~~~~~~~~~~ 151 (198)
T KOG0483|consen 129 DRLQSEVQELVAELSSLKREMQK 151 (198)
T ss_pred hHHHHHHHHHHHHHhhhhhhhcc
Confidence 99999999999999987765543
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=1.6e-18 Score=157.10 Aligned_cols=62 Identities=37% Similarity=0.695 Sum_probs=57.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 32 SQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 32 ~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
++.||.|+.||..|+.+||+.|+.++|++..+|+|||..|+|+|+||+|||||||+||||..
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 34567777899999999999999999999999999999999999999999999999999865
No 3
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.72 E-value=4.1e-18 Score=156.79 Aligned_cols=58 Identities=38% Similarity=0.574 Sum_probs=55.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDY 98 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~~~~ 98 (254)
|+..|+.+||+.|..++|++..+|++||..|.|+++||||||||||-|.||+++++..
T Consensus 160 FSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 160 FSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred cchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 9999999999999999999999999999999999999999999999999998866653
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.69 E-value=3.7e-17 Score=151.54 Aligned_cols=62 Identities=34% Similarity=0.607 Sum_probs=56.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 32 SQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 32 ~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
+++|+.|+.||..||..||+.|++.+|++..+|++||..|||+..||++||||||+|||+..
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 34444555699999999999999999999999999999999999999999999999999975
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.68 E-value=1.2e-17 Score=153.63 Aligned_cols=64 Identities=36% Similarity=0.526 Sum_probs=58.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHH
Q 041877 32 SQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLE 95 (254)
Q Consensus 32 ~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~ 95 (254)
+..||||.-+|..|+.+||+.|..|.|+..+.|.+|++.|+|++|||+|||||||+|.||..++
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 4456777779999999999999999999999999999999999999999999999999997643
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.66 E-value=1.1e-16 Score=136.54 Aligned_cols=64 Identities=33% Similarity=0.486 Sum_probs=58.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHHH
Q 041877 33 QVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEK 96 (254)
Q Consensus 33 ~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~~ 96 (254)
+.+|.|+.||.+||..||..|+.++|....+|++||..|+|++.||+|||||||.|.||.+.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 3455666799999999999999999999999999999999999999999999999999987554
No 7
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.66 E-value=1.1e-16 Score=125.86 Aligned_cols=63 Identities=22% Similarity=0.437 Sum_probs=57.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 31 GSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 31 ~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
.++++|-|+.||..||.+||+.|...+||++-.|++||.++.|++.+|+|||||||+|.|++.
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 344566677799999999999999999999999999999999999999999999999999865
No 8
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.64 E-value=2.9e-16 Score=137.56 Aligned_cols=59 Identities=37% Similarity=0.621 Sum_probs=54.5
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 35 GEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 35 ~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
||.|+.|+..|+..||..|+...|++..+|..||++|.|++.||+|||||||.||||+-
T Consensus 105 KktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 105 KKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 33444599999999999999999999999999999999999999999999999999863
No 9
>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=99.63 E-value=5.7e-16 Score=108.54 Aligned_cols=57 Identities=40% Similarity=0.606 Sum_probs=54.5
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 35 GEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 35 ~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
+++|++||.+|+.+||.+|..++||+..++..||..|||++.+|++||+|||+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 467888999999999999999999999999999999999999999999999999885
No 10
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.63 E-value=5.1e-16 Score=136.89 Aligned_cols=68 Identities=31% Similarity=0.532 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHH
Q 041877 25 EDLSDDGSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTK 92 (254)
Q Consensus 25 ~~~~~~~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~ 92 (254)
......+++.|+.|+.++.-||..|.+.|++++|+...+|.+||..|||+..||+|||||||.|.||.
T Consensus 113 ~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 113 RRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred eccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 33445566667777789999999999999999999999999999999999999999999999999975
No 11
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.61 E-value=4.5e-16 Score=136.50 Aligned_cols=65 Identities=23% Similarity=0.396 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 29 DDGSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 29 ~~~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
...++.||.|++||..|+.+||+.|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|+.+
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 34556677888999999999999999999999999999999999999999999999999999876
No 12
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.57 E-value=1.3e-15 Score=136.94 Aligned_cols=53 Identities=42% Similarity=0.604 Sum_probs=51.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
+|..|..+||+.|...+|..+.++.+||..|||+||||+|||||||+|+||..
T Consensus 206 YTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 89999999999999999999999999999999999999999999999999865
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.57 E-value=3.1e-15 Score=130.32 Aligned_cols=59 Identities=32% Similarity=0.504 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 35 GEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 35 ~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
|+.|+-||..||..||+-|...+|+++.+|.+++..|.|++.||+|||||||+|.||.+
T Consensus 145 RkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 145 RKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 34455699999999999999999999999999999999999999999999999999876
No 14
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.55 E-value=1.3e-14 Score=131.65 Aligned_cols=89 Identities=22% Similarity=0.380 Sum_probs=78.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041877 31 GSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDYEVLKKQFEALKA 110 (254)
Q Consensus 31 ~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~~~~~~lk~~~~~l~~ 110 (254)
....+|.|+.+|+.||+.|...|+..++|....|++|+.++||..|.|+|||||||||.||.++..-...|.+.|..+|.
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK~ 243 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMKR 243 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhhc
Confidence 34457778889999999999999999999999999999999999999999999999999999988888899999999887
Q ss_pred hhHHHHHHHH
Q 041877 111 DNDSLQAQNK 120 (254)
Q Consensus 111 e~~~l~~e~~ 120 (254)
. ..-+++++
T Consensus 244 s-gs~r~ekd 252 (383)
T KOG4577|consen 244 S-GSSRAEKD 252 (383)
T ss_pred c-CCcccccc
Confidence 6 33344443
No 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.54 E-value=1.2e-14 Score=130.36 Aligned_cols=57 Identities=30% Similarity=0.520 Sum_probs=53.7
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHH
Q 041877 38 KKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQL 94 (254)
Q Consensus 38 R~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~ 94 (254)
|+.||..|+..||+.|+..+||+...|+-||.++.|.+.+|+|||||||+||||...
T Consensus 145 RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred cchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 445999999999999999999999999999999999999999999999999998753
No 16
>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=99.50 E-value=4.6e-14 Score=98.58 Aligned_cols=57 Identities=46% Similarity=0.714 Sum_probs=53.6
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHH
Q 041877 36 EKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTK 92 (254)
Q Consensus 36 rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~ 92 (254)
+++..++..|+.+||.+|..++||+..++..||..+||++++|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 456789999999999999999999999999999999999999999999999998763
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.49 E-value=5.1e-14 Score=97.76 Aligned_cols=55 Identities=44% Similarity=0.762 Sum_probs=51.5
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 36 EKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 36 rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
+.|.+|+.+|+.+||..|..++||+..++..||..+||+..+|+.||+|||++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4566799999999999999999999999999999999999999999999998754
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.48 E-value=5.1e-14 Score=118.94 Aligned_cols=64 Identities=33% Similarity=0.567 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 30 DGSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 30 ~~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
..+..+++|+|.|..|+.+|++.|+.++||+...|..|+..|+|+++-|+|||||||++.|+..
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~ 110 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKR 110 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhc
Confidence 3445678889999999999999999999999999999999999999999999999999999865
No 19
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.43 E-value=5.9e-14 Score=125.99 Aligned_cols=64 Identities=36% Similarity=0.573 Sum_probs=57.1
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHHHHHHHH
Q 041877 38 KKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDYEVL 101 (254)
Q Consensus 38 R~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~~~~~~l 101 (254)
|+-||.+||..|...|+.+.|+...+|.+||.+|+|.+.||+|||||+|+|.|+..-.+....+
T Consensus 250 RTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~ 313 (342)
T KOG0493|consen 250 RTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLAL 313 (342)
T ss_pred cccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhh
Confidence 4459999999999999999999999999999999999999999999999999987655444333
No 20
>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=99.43 E-value=1.6e-13 Score=97.91 Aligned_cols=52 Identities=13% Similarity=0.309 Sum_probs=49.6
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCC----CCHHHHHHHHHHhCCChhhhhhhhhhhH
Q 041877 35 GEKKKRLNLEQVKALEKSFELGNK----LEPERKLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 35 ~rkR~r~t~~Ql~~LE~~F~~~~y----p~~~~r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
+|.|+.||.+|+..||.+|+..+| |+...+.+||..|||++++|+|||||-+
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 677888999999999999999999 9999999999999999999999999964
No 21
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.42 E-value=7.3e-14 Score=127.68 Aligned_cols=65 Identities=35% Similarity=0.522 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHH
Q 041877 31 GSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLE 95 (254)
Q Consensus 31 ~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~ 95 (254)
..+.||=|+-||.+|+..||+.|-+.+|-+..+|.+||..|+|.+.-|+|||||||+|.||+.+.
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 44567778889999999999999999999999999999999999999999999999999998754
No 22
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.41 E-value=1.2e-13 Score=126.50 Aligned_cols=62 Identities=21% Similarity=0.510 Sum_probs=56.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHH
Q 041877 33 QVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQL 94 (254)
Q Consensus 33 ~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~ 94 (254)
++||.|+-||..|+.+||..|+++.||+...|++||..++|++.+|+|||+|||+|||+..+
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 34555666999999999999999999999999999999999999999999999999998753
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.34 E-value=3.2e-13 Score=114.08 Aligned_cols=59 Identities=36% Similarity=0.537 Sum_probs=54.8
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 35 GEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 35 ~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
++-|+.|+..|+..||+.|+...|++..+|.+||..|+|++.||+.||||||+|.||.+
T Consensus 101 ~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 101 RKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred hhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 34456699999999999999999999999999999999999999999999999999865
No 24
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.32 E-value=6.8e-13 Score=125.14 Aligned_cols=61 Identities=26% Similarity=0.404 Sum_probs=56.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 33 QVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 33 ~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
++||||+.|.......||++|.+|++|+..+...||.+|+|...+|+|||||||.|.||..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 4566667788999999999999999999999999999999999999999999999999864
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.28 E-value=2.4e-12 Score=113.26 Aligned_cols=63 Identities=32% Similarity=0.604 Sum_probs=57.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 31 GSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 31 ~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
.++++..|..|+-.|+..||+.|+..+|+-.++|.+||-.+|+++.||+|||||||.|||++.
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 344455667799999999999999999999999999999999999999999999999999875
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.15 E-value=1.7e-11 Score=107.09 Aligned_cols=62 Identities=24% Similarity=0.298 Sum_probs=57.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 32 SQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 32 ~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
...++.|+.|+..|+.+||+.|+..+||+...|+.||..+++++..|+|||||||++|++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 34566777899999999999999999999999999999999999999999999999999864
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.96 E-value=7.6e-10 Score=104.65 Aligned_cols=62 Identities=27% Similarity=0.534 Sum_probs=56.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 32 SQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 32 ~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
+..++.|+.|+..|+..||+.|+.++||++..|++||.++++++.+|+|||+|||+++++..
T Consensus 174 ~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 174 RGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 33455567899999999999999999999999999999999999999999999999999864
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.94 E-value=3e-10 Score=103.61 Aligned_cols=64 Identities=22% Similarity=0.419 Sum_probs=58.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 30 DGSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 30 ~~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
.+..+||||+.+.....+.||.+|..+++|+.+....||++|+|....|+|||||+|.|-||..
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 3455678888899999999999999999999999999999999999999999999999988853
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.66 E-value=2.3e-08 Score=90.68 Aligned_cols=51 Identities=29% Similarity=0.432 Sum_probs=46.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
|...-..+|..+|..++||++.++.+||+.+||+..||-.||+|||.|.|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 344466799999999999999999999999999999999999999999884
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.48 E-value=7.3e-08 Score=87.09 Aligned_cols=59 Identities=24% Similarity=0.417 Sum_probs=55.0
Q ss_pred CCCCCCCCCHHHHHHHHHHhh---cCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHH
Q 041877 34 VGEKKKRLNLEQVKALEKSFE---LGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTK 92 (254)
Q Consensus 34 ~~rkR~r~t~~Ql~~LE~~F~---~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~ 92 (254)
.+|||+.|+..-..+|..+|. .++||+.+.+++||+++|++..||-.||.|+|-+.|+.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 578888899999999999997 68899999999999999999999999999999998874
No 31
>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=98.32 E-value=5.4e-07 Score=59.66 Aligned_cols=34 Identities=38% Similarity=0.544 Sum_probs=29.0
Q ss_pred cCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHH
Q 041877 55 LGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88 (254)
Q Consensus 55 ~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak 88 (254)
.++||+..++.+||+++||+..||..||-|.|.+
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 4799999999999999999999999999999865
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.93 E-value=1.3e-05 Score=69.91 Aligned_cols=62 Identities=31% Similarity=0.537 Sum_probs=56.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 32 SQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 32 ~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
.+.++.++.++..|+..|+..|...++|+...+.+|+..+|+.++.|++||+|+|++.++..
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 34455566789999999999999999999999999999999999999999999999999864
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.82 E-value=3.1e-05 Score=76.37 Aligned_cols=60 Identities=18% Similarity=0.206 Sum_probs=53.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHH
Q 041877 30 DGSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARW 89 (254)
Q Consensus 30 ~~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~ 89 (254)
..-+.||.|..||..|.+.|..+|+.+++|+.+..+.|+.+|+|..+-|..||=|-|.|.
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 344455566779999999999999999999999999999999999999999999988774
No 34
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=97.44 E-value=0.00031 Score=47.68 Aligned_cols=42 Identities=52% Similarity=0.782 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhccC
Q 041877 92 KQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNKD 133 (254)
Q Consensus 92 ~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 133 (254)
++++++|+.||..|+.|++++++|..|++.|++++..|+...
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl 42 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKL 42 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 468999999999999999999999999999999999998764
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.17 E-value=0.0006 Score=73.11 Aligned_cols=66 Identities=27% Similarity=0.384 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHH
Q 041877 29 DDGSQVGEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQL 94 (254)
Q Consensus 29 ~~~~~~~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~ 94 (254)
.++-.+++.|++++..||..|..+|....||...+.+.|-..+++.++.|++||||-|+|.|+..+
T Consensus 898 ~~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 898 PDGMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred chhhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 334445778889999999999999999999999999999999999999999999999999998654
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.67 E-value=0.0015 Score=46.40 Aligned_cols=42 Identities=21% Similarity=0.355 Sum_probs=31.4
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHH
Q 041877 46 VKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRA 87 (254)
Q Consensus 46 l~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRa 87 (254)
+..|+.+|...+++.......|..+.+|+..||+.||-.|+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 567999999999999999999999999999999999976543
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.54 E-value=0.0027 Score=59.47 Aligned_cols=58 Identities=29% Similarity=0.358 Sum_probs=48.5
Q ss_pred CCCCCCCHHHHHHHHHHhh---cCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 36 EKKKRLNLEQVKALEKSFE---LGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 36 rkR~r~t~~Ql~~LE~~F~---~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
++++.+....+.+|+.+.. ..+||+...+..||+++||+..||.+||-|.|-|..+.-
T Consensus 241 r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 241 RPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 3344599999999998743 357999999999999999999999999999988766544
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.00 E-value=0.075 Score=54.72 Aligned_cols=48 Identities=19% Similarity=0.331 Sum_probs=45.3
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 46 VKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 46 l~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
+.+|..+|..|..|...+...+|.+.||..+.|+.||+++++......
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999999988755
No 39
>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=93.95 E-value=0.14 Score=35.53 Aligned_cols=47 Identities=28% Similarity=0.456 Sum_probs=35.1
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhH
Q 041877 35 GEKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 35 ~rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
+++|+.+|.++...+-..++... ....||+.+|+...+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46777899998888878887776 477899999999999999998853
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.75 E-value=0.85 Score=36.56 Aligned_cols=44 Identities=25% Similarity=0.430 Sum_probs=29.9
Q ss_pred CCCCCCCHHHHH-HHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhh
Q 041877 36 EKKKRLNLEQVK-ALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQN 84 (254)
Q Consensus 36 rkR~r~t~~Ql~-~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQN 84 (254)
++|++|+.++.. ++...+. +.+ ...++|+.+|+++..|..|.+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 345678888644 4444443 332 3567899999999999999654
No 41
>smart00340 HALZ homeobox associated leucin zipper.
Probab=89.17 E-value=0.93 Score=30.41 Aligned_cols=32 Identities=41% Similarity=0.521 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 041877 93 QLEKDYEVLKKQFEALKADNDSLQAQNKKLHA 124 (254)
Q Consensus 93 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~ 124 (254)
+.+-+++-+|+-++.|..||..|+.|...|++
T Consensus 2 QTEvdCe~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 2 QTEVDCELLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56778999999999999999888887765543
No 42
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=89.13 E-value=4.7 Score=36.73 Aligned_cols=33 Identities=33% Similarity=0.360 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHh
Q 041877 96 KDYEVLKKQFEALKADNDSLQAQNKKLHAELVS 128 (254)
Q Consensus 96 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~ 128 (254)
.++..|-.+.+.|..+|+.|++.|+.|.++..+
T Consensus 97 ~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~e 129 (292)
T KOG4005|consen 97 YEIKDLTEENEILQNENDSLRAINESLLAKNHE 129 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Confidence 333444555555555555555554444444333
No 43
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=82.61 E-value=27 Score=29.03 Aligned_cols=77 Identities=25% Similarity=0.359 Sum_probs=45.6
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHH-HHhCCChhhhhhhhhhhHHH----------HHH----HHHHHHHHHHHH
Q 041877 39 KRLNLEQVKALEKSFELGNKLEPERKLQLA-RALGLQPRQIAIWFQNRRAR----------WKT----KQLEKDYEVLKK 103 (254)
Q Consensus 39 ~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA-~~LgL~~rqV~vWFQNRRak----------~Kr----~~~~~~~~~lk~ 103 (254)
.+|+.++|..| ..| +|= +.-|++...|-.|=|.||+- .|+ ..++++...|.+
T Consensus 22 d~lsDd~Lvsm------------SVR-eLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~q 88 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVR-ELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQ 88 (135)
T ss_pred CCcCHHHHHHh------------hHH-HHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67888887766 223 333 34488999999999888853 222 223344444555
Q ss_pred HHHHHHhhhHHHHHHHHHHHHHHHh
Q 041877 104 QFEALKADNDSLQAQNKKLHAELVS 128 (254)
Q Consensus 104 ~~~~l~~e~~~l~~e~~~l~~e~~~ 128 (254)
+++.|+.|+..++.|.+-++.....
T Consensus 89 qv~~L~~e~s~~~~E~da~k~k~e~ 113 (135)
T KOG4196|consen 89 QVEKLKEENSRLRRELDAYKSKYEA 113 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555665555555555544444433
No 44
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=82.43 E-value=4.3 Score=27.45 Aligned_cols=33 Identities=33% Similarity=0.689 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 041877 94 LEKDYEVLKKQFEALKADNDSLQAQNKKLHAEL 126 (254)
Q Consensus 94 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 126 (254)
+...++.++..++.|..++..|+++...|...+
T Consensus 10 LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl 42 (45)
T PF02183_consen 10 LKASYDSLKAEYDSLKKENEKLRAEVQELKEKL 42 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 455677888888888888888888887776554
No 45
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=80.78 E-value=4.7 Score=31.90 Aligned_cols=46 Identities=24% Similarity=0.333 Sum_probs=20.5
Q ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 041877 76 RQIAIWFQNRRARWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKL 122 (254)
Q Consensus 76 rqV~vWFQNRRak~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l 122 (254)
-++..||...-- .+-.+...+.+.++.+++.++.+|..|+.+...|
T Consensus 15 l~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L 60 (105)
T PRK00888 15 LQYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDL 60 (105)
T ss_pred HHHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356688865321 1222233344444444444444444444444433
No 46
>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=80.33 E-value=0.85 Score=32.79 Aligned_cols=46 Identities=20% Similarity=0.317 Sum_probs=28.0
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 041877 36 EKKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNR 85 (254)
Q Consensus 36 rkR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNR 85 (254)
++|++||.++...+-..+.. ......++|+.+||++..+..|-+--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHHH
Confidence 45678999966655444411 23557789999999999999996543
No 47
>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=78.56 E-value=6.3 Score=26.21 Aligned_cols=40 Identities=13% Similarity=0.179 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhh
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQN 84 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQN 84 (254)
.++..+..+|...|. ....-.++|..+|++...|+.+...
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHH
Confidence 477888999999982 2234678999999999999887643
No 48
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=77.06 E-value=12 Score=27.84 Aligned_cols=36 Identities=31% Similarity=0.415 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhh
Q 041877 95 EKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLK 130 (254)
Q Consensus 95 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 130 (254)
-..+..++.+++.|+.+|..+..++..|..++..|+
T Consensus 17 veti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~ 52 (72)
T PF06005_consen 17 VETIALLQMENEELKEKNNELKEENEELKEENEQLK 52 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 334445555555555554444444444444444443
No 49
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=74.88 E-value=18 Score=25.56 Aligned_cols=37 Identities=30% Similarity=0.488 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhc
Q 041877 95 EKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKN 131 (254)
Q Consensus 95 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 131 (254)
...+..|...+..|..++..|..++..|..++..|+.
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~ 61 (64)
T PF00170_consen 25 KQYIEELEEKVEELESENEELKKELEQLKKEIQSLKS 61 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455667777777888888888877777777777654
No 50
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=74.19 E-value=4.6 Score=27.85 Aligned_cols=42 Identities=19% Similarity=0.213 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHH
Q 041877 63 RKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDYEVLKKQ 104 (254)
Q Consensus 63 ~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~~~~~~lk~~ 104 (254)
...+||+.+|++...|..|+.++..........+-...+.-.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~ 53 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCS 53 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCC
Confidence 467899999999999999999886666666555554444433
No 51
>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=73.71 E-value=5.3 Score=25.45 Aligned_cols=43 Identities=14% Similarity=0.176 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRA 87 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRa 87 (254)
.++..+..+++..|... ..-.++|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36777778887776422 23567899999999999999865443
No 52
>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=72.63 E-value=6.2 Score=27.56 Aligned_cols=40 Identities=25% Similarity=0.291 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHhhcCCC--CCHHHHHHHHHHhCCChhhhhh
Q 041877 41 LNLEQVKALEKSFELGNK--LEPERKLQLARALGLQPRQIAI 80 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~y--p~~~~r~~LA~~LgL~~rqV~v 80 (254)
+|..|..+|...|+..-| |-...-.+||+.||++..-|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 578899999999987665 6677778999999999876543
No 53
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=71.29 E-value=13 Score=29.83 Aligned_cols=38 Identities=37% Similarity=0.468 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhh
Q 041877 92 KQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSL 129 (254)
Q Consensus 92 ~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 129 (254)
.....+...+|.....+.+||..|+.||++|+..+..+
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~ 55 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45667788899999999999999999999999887764
No 54
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=70.20 E-value=15 Score=29.30 Aligned_cols=40 Identities=35% Similarity=0.487 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhc
Q 041877 92 KQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKN 131 (254)
Q Consensus 92 ~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 131 (254)
..+..+...+|.+...+.+||..|+.||.+|+..+..+..
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4566777888888999999999999999988887766533
No 55
>smart00338 BRLZ basic region leucin zipper.
Probab=69.71 E-value=36 Score=23.98 Aligned_cols=38 Identities=32% Similarity=0.536 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhcc
Q 041877 95 EKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNK 132 (254)
Q Consensus 95 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 132 (254)
......|..++..|..+|..|..+...|..++..|+..
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~ 62 (65)
T smart00338 25 KAEIEELERKVEQLEAENERLKKEIERLRRELEKLKSE 62 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44556778888888888888888888888888877754
No 56
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=67.83 E-value=18 Score=33.82 Aligned_cols=41 Identities=27% Similarity=0.375 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhcc
Q 041877 92 KQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNK 132 (254)
Q Consensus 92 ~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 132 (254)
++++.+.+.+-.+++.|...|+.|+.+...|+.|+..||..
T Consensus 244 qKkRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKql 284 (294)
T KOG4571|consen 244 QKKRAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQL 284 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455667788888888888888888888888888887753
No 57
>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=67.19 E-value=18 Score=20.32 Aligned_cols=39 Identities=21% Similarity=0.403 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 041877 39 KRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWF 82 (254)
Q Consensus 39 ~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWF 82 (254)
+.++.++...+...|... + ...++|+.+|++...|..|.
T Consensus 4 ~~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 346667666666666532 2 45688999999998888773
No 58
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=66.82 E-value=15 Score=33.75 Aligned_cols=34 Identities=24% Similarity=0.473 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhcc
Q 041877 99 EVLKKQFEALKADNDSLQAQNKKLHAELVSLKNK 132 (254)
Q Consensus 99 ~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 132 (254)
...+.....|..||..|+.+++.|+.|+..++..
T Consensus 218 ~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~ 251 (269)
T KOG3119|consen 218 DEMAHRVAELEKENEALRTQVEQLKKELATLRRL 251 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455566667777777777777777777776654
No 59
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=65.99 E-value=38 Score=23.83 Aligned_cols=39 Identities=26% Similarity=0.334 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 041877 88 RWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAEL 126 (254)
Q Consensus 88 k~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 126 (254)
+.....++..+..+....+.|..+...|..+...|..++
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 25 KQYIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 334456666777777888888888888887777777665
No 60
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=62.05 E-value=44 Score=24.72 Aligned_cols=43 Identities=26% Similarity=0.327 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhh
Q 041877 88 RWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLK 130 (254)
Q Consensus 88 k~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 130 (254)
-.....+..+.+.++.+...+..++..|..+|.+|+.+.....
T Consensus 17 veti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~ 59 (72)
T PF06005_consen 17 VETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQ 59 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344566777888888888888888888888888877765543
No 61
>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=61.39 E-value=6.4 Score=28.31 Aligned_cols=19 Identities=26% Similarity=0.562 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCChhhhhhh
Q 041877 63 RKLQLARALGLQPRQIAIW 81 (254)
Q Consensus 63 ~r~~LA~~LgL~~rqV~vW 81 (254)
.-.+||.+||+++.+|+.|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 3467899999999999999
No 62
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=61.14 E-value=17 Score=26.06 Aligned_cols=44 Identities=20% Similarity=0.373 Sum_probs=23.2
Q ss_pred CCCCCHH-HHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 041877 38 KKRLNLE-QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQ 83 (254)
Q Consensus 38 R~r~t~~-Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQ 83 (254)
|+.|+.. -|.+++.+. ....--...|. -|++.|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~-~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAE-KDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHH-H-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHH-HccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4557776 445555444 33333333444 49999999999999954
No 63
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=60.30 E-value=49 Score=27.62 Aligned_cols=48 Identities=15% Similarity=0.118 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 38 KKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 38 R~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
...++..|..+|...+ . .....++|..||++...|..|-.+.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr~--~----GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--R----GLTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4568999999997743 2 2335689999999999999998866665554
No 64
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=56.54 E-value=61 Score=22.11 Aligned_cols=26 Identities=23% Similarity=0.431 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHH
Q 041877 98 YEVLKKQFEALKADNDSLQAQNKKLH 123 (254)
Q Consensus 98 ~~~lk~~~~~l~~e~~~l~~e~~~l~ 123 (254)
...+...+..|..+|..|..++..|.
T Consensus 27 ~~~le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 27 EEELEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34455555555555555555554444
No 65
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=55.87 E-value=65 Score=24.45 Aligned_cols=37 Identities=27% Similarity=0.490 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhh
Q 041877 93 QLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSL 129 (254)
Q Consensus 93 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 129 (254)
.+......+-..++.++.+++.|..||+-|+.=+..|
T Consensus 27 ~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL 63 (80)
T PF10224_consen 27 ELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL 63 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344445555566666666666666666666554443
No 66
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=55.30 E-value=16 Score=24.04 Aligned_cols=40 Identities=23% Similarity=0.297 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 041877 39 KRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQ 83 (254)
Q Consensus 39 ~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQ 83 (254)
+.||.++...++..+... ....+||+.||.++.-|..+.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 468889999998887533 3456799999999998877653
No 67
>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=50.90 E-value=42 Score=22.26 Aligned_cols=41 Identities=15% Similarity=0.169 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
++..+..++...|- ....-.++|..+|+++..|+.|...-|
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45566666655443 334567899999999999999986433
No 68
>smart00338 BRLZ basic region leucin zipper.
Probab=50.49 E-value=76 Score=22.30 Aligned_cols=37 Identities=32% Similarity=0.471 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 041877 90 KTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAEL 126 (254)
Q Consensus 90 Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 126 (254)
....++.....+..+...|..+...+..++..|..++
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445666666677777777777777777776666554
No 69
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=47.49 E-value=48 Score=26.72 Aligned_cols=35 Identities=29% Similarity=0.381 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Q 041877 93 QLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELV 127 (254)
Q Consensus 93 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~ 127 (254)
.+..+...+|+....+..||..|+-||++|+..+.
T Consensus 19 ~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~ 53 (114)
T COG4467 19 VLLAELGGLKQHLGSLVEENTALRLENEKLRERLG 53 (114)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhC
Confidence 44556677788888888888888888887776543
No 70
>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=46.28 E-value=52 Score=22.36 Aligned_cols=45 Identities=11% Similarity=0.114 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
+||..++.+|.-...-. ...++|..++++++.|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 57888888887766433 3678999999999999998766555544
No 71
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=46.21 E-value=38 Score=29.51 Aligned_cols=39 Identities=21% Similarity=0.330 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHhhcCC--CCCHHHHHHHHHHhCCChhhh
Q 041877 40 RLNLEQVKALEKSFELGN--KLEPERKLQLARALGLQPRQI 78 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~--yp~~~~r~~LA~~LgL~~rqV 78 (254)
.+|..|+++|...|+..= +|-...-.+||++||+++.-+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 699999999999998765 477777899999999998654
No 72
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=46.03 E-value=74 Score=32.44 Aligned_cols=33 Identities=27% Similarity=0.397 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhc
Q 041877 99 EVLKKQFEALKADNDSLQAQNKKLHAELVSLKN 131 (254)
Q Consensus 99 ~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 131 (254)
..++..+.++..||+.|++||..|+..+..+-.
T Consensus 305 ~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~ 337 (655)
T KOG4343|consen 305 LGLEARLQALLSENEQLKKENATLKRQLDELVS 337 (655)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence 445666666666666666666666655555443
No 73
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=45.13 E-value=85 Score=25.05 Aligned_cols=37 Identities=35% Similarity=0.451 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhcc
Q 041877 96 KDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNK 132 (254)
Q Consensus 96 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 132 (254)
..+..+..+......+++.|.+++..|.+++..|++.
T Consensus 50 ~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 50 ADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3333444444455555555555555555555555443
No 74
>PF15058 Speriolin_N: Speriolin N terminus
Probab=44.88 E-value=1.5e+02 Score=26.21 Aligned_cols=35 Identities=31% Similarity=0.439 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhcc
Q 041877 97 DYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNK 132 (254)
Q Consensus 97 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 132 (254)
.|+-+..+++.+..||..|+.+..-+ .|+.+||..
T Consensus 6 ~yeGlrhqierLv~ENeeLKKlVrLi-rEN~eLksa 40 (200)
T PF15058_consen 6 NYEGLRHQIERLVRENEELKKLVRLI-RENHELKSA 40 (200)
T ss_pred chHHHHHHHHHHHhhhHHHHHHHHHH-HHHHHHHHH
Confidence 46777888888888888888776544 456666665
No 75
>PRK04217 hypothetical protein; Provisional
Probab=44.31 E-value=68 Score=25.67 Aligned_cols=44 Identities=14% Similarity=0.138 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak 88 (254)
.++.+|..++...|...- ...+||+.+|++...|...+..-+.+
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 478888888877764333 46789999999999998877644333
No 76
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=43.75 E-value=85 Score=20.02 Aligned_cols=40 Identities=18% Similarity=0.199 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhh
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNR 85 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNR 85 (254)
.++..+...+...+.- ....++|..+|++...|..|...-
T Consensus 3 ~l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 3 SLTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4677777777664321 245789999999999999887643
No 77
>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=43.75 E-value=21 Score=22.95 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhhhhhhhhhh
Q 041877 64 KLQLARALGLQPRQIAIWFQNR 85 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQNR 85 (254)
..++|+.+|++++.|+.|.+.-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997554
No 78
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=43.32 E-value=38 Score=24.33 Aligned_cols=29 Identities=34% Similarity=0.525 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 041877 96 KDYEVLKKQFEALKADNDSLQAQNKKLHA 124 (254)
Q Consensus 96 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~ 124 (254)
.+.+.+|.++..|...+..|+.||..|+.
T Consensus 14 EEVevLK~~I~eL~~~n~~Le~EN~~Lk~ 42 (59)
T PF01166_consen 14 EEVEVLKEQIAELEERNSQLEEENNLLKQ 42 (59)
T ss_dssp TSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45677888888888888888777766654
No 79
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=43.21 E-value=1e+02 Score=23.41 Aligned_cols=24 Identities=29% Similarity=0.429 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHH
Q 041877 95 EKDYEVLKKQFEALKADNDSLQAQ 118 (254)
Q Consensus 95 ~~~~~~lk~~~~~l~~e~~~l~~e 118 (254)
...+..++.+++.++..|..+..+
T Consensus 17 vdtI~LLqmEieELKekn~~L~~e 40 (79)
T PRK15422 17 IDTITLLQMEIEELKEKNNSLSQE 40 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444555555555554444443
No 80
>PRK10072 putative transcriptional regulator; Provisional
Probab=42.81 E-value=41 Score=26.16 Aligned_cols=41 Identities=22% Similarity=0.344 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRA 87 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRa 87 (254)
+.+...+..|...-.. ...+||+.+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3466666666443322 2678999999999999999987764
No 81
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=41.84 E-value=79 Score=22.49 Aligned_cols=30 Identities=33% Similarity=0.586 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 041877 93 QLEKDYEVLKKQFEALKADNDSLQAQNKKL 122 (254)
Q Consensus 93 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l 122 (254)
....+...++.+++.++.+++.|+.+.+.|
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334455566666666666666665555554
No 82
>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=41.78 E-value=66 Score=24.59 Aligned_cols=45 Identities=16% Similarity=0.200 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
++..+...+...|- ......+||+.+|+++..|..+...-+.+.|
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 44555555544332 2234568999999999999988765444433
No 83
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=41.33 E-value=89 Score=22.81 Aligned_cols=31 Identities=35% Similarity=0.385 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHh
Q 041877 98 YEVLKKQFEALKADNDSLQAQNKKLHAELVS 128 (254)
Q Consensus 98 ~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~ 128 (254)
.+.+-..++.|+.+|..|+.+...+..|...
T Consensus 9 le~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~ 39 (65)
T TIGR02449 9 VEHLLEYLERLKSENRLLRAQEKTWREERAQ 39 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444444444444333
No 84
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=41.22 E-value=1.6e+02 Score=22.36 Aligned_cols=44 Identities=23% Similarity=0.326 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhc
Q 041877 88 RWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKN 131 (254)
Q Consensus 88 k~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 131 (254)
+..+..+.++...++..++.|....+..+.|+++|..|+.-|..
T Consensus 15 ~e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~ 58 (80)
T PF10224_consen 15 KEEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQ 58 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666778888888888888888888888888888877654
No 85
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=41.00 E-value=75 Score=25.27 Aligned_cols=44 Identities=11% Similarity=0.128 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARW 89 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~ 89 (254)
++..+..++...|-.. ..-.++|..+|+++..|+.|...-|.+.
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5566666665544332 3367899999999999999876444443
No 86
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=40.26 E-value=1.5e+02 Score=22.85 Aligned_cols=39 Identities=13% Similarity=0.030 Sum_probs=27.8
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHH
Q 041877 37 KKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRA 87 (254)
Q Consensus 37 kR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRa 87 (254)
.+++|+.+++..|.. ...|.+.+|++-..|+.+..+...
T Consensus 35 g~R~Yt~~di~~l~~------------I~~llr~~G~~l~~i~~~l~~~~~ 73 (99)
T cd04765 35 GRRYYRPKDVELLLL------------IKHLLYEKGYTIEGAKQALKEDGA 73 (99)
T ss_pred CCeeeCHHHHHHHHH------------HHHHHHHCCCCHHHHHHHHHhccc
Confidence 456799999988843 334567888998888888765433
No 87
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=39.98 E-value=14 Score=37.84 Aligned_cols=46 Identities=13% Similarity=0.047 Sum_probs=32.1
Q ss_pred HHHHHhhcCCCCCHHHHHHHHHHhCCC-------hhhhhhhhhhhHHHHHHHH
Q 041877 48 ALEKSFELGNKLEPERKLQLARALGLQ-------PRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 48 ~LE~~F~~~~yp~~~~r~~LA~~LgL~-------~rqV~vWFQNRRak~Kr~~ 93 (254)
+-+.+|.+++.+......+--..+.|. .+-|+.||.+||+++++.+
T Consensus 706 v~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 706 VKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 335567777777766665555555443 4569999999999988754
No 88
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=39.58 E-value=32 Score=32.91 Aligned_cols=26 Identities=27% Similarity=0.479 Sum_probs=11.3
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHH
Q 041877 100 VLKKQFEALKADNDSLQAQNKKLHAE 125 (254)
Q Consensus 100 ~lk~~~~~l~~e~~~l~~e~~~l~~e 125 (254)
.|+.+.+.|+.|+..|+.+..+|+++
T Consensus 36 aLr~EN~~LKkEN~~Lk~eVerLE~e 61 (420)
T PF07407_consen 36 ALRMENHSLKKENNDLKIEVERLENE 61 (420)
T ss_pred hHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444444333
No 89
>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=39.27 E-value=14 Score=27.60 Aligned_cols=35 Identities=14% Similarity=0.208 Sum_probs=26.3
Q ss_pred HHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhh
Q 041877 50 EKSFELGNKLEPERKLQLARALGLQPRQIAIWFQN 84 (254)
Q Consensus 50 E~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQN 84 (254)
+..|....|-..-...+||+.+|+++.-|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34455555445556789999999999999999864
No 90
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=39.17 E-value=43 Score=26.12 Aligned_cols=34 Identities=32% Similarity=0.558 Sum_probs=19.2
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 46 VKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 46 l~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
+....-.|+.++||...--.. | =.|||.+||+.+
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq 47 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQ 47 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHH
Confidence 455666799999997441111 1 158999999875
No 91
>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]
Probab=39.09 E-value=1.8e+02 Score=30.94 Aligned_cols=45 Identities=33% Similarity=0.502 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhc
Q 041877 87 ARWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKN 131 (254)
Q Consensus 87 ak~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 131 (254)
+..++..+..+.+.+|++++++..+.+.+...++.|..++..|+.
T Consensus 214 Ale~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~~ 258 (916)
T KOG0249|consen 214 ALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLRR 258 (916)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence 455667778888889999999988888888888888888887774
No 92
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=38.99 E-value=46 Score=26.86 Aligned_cols=45 Identities=16% Similarity=0.192 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
++..+..+|...|. ....-.+||..+|+++..|..|...-|.+.|
T Consensus 126 L~~~~r~i~~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYV-----EGLSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 44444444444432 2233578999999999999999865555444
No 93
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=38.98 E-value=47 Score=26.90 Aligned_cols=45 Identities=13% Similarity=-0.011 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
+++.+..+|...|-. ...-.++|..+|+++..|+.|...-+.+.|
T Consensus 129 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 129 LPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 666677777665432 223568899999999999998764333333
No 94
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=38.94 E-value=63 Score=27.19 Aligned_cols=46 Identities=13% Similarity=0.136 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
++..+..+|...|... ..-.++|+.||++...|+.+...-|.+.|.
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 5666666665544222 345689999999999999988655544443
No 95
>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=37.42 E-value=50 Score=21.62 Aligned_cols=39 Identities=15% Similarity=0.395 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhh
Q 041877 39 KRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWF 82 (254)
Q Consensus 39 ~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWF 82 (254)
+.++.++...+-+.+... + ...+||+.+|++...|..++
T Consensus 4 ~~~~~~~~~~i~~l~~~G-~----si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-M----SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHH
Confidence 346666666666666655 2 36789999999998887665
No 96
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=37.19 E-value=50 Score=27.18 Aligned_cols=46 Identities=15% Similarity=0.328 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
++..+..++...| .....-.+||..+|+++..|+++...-|.+.|.
T Consensus 130 L~~~~r~i~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAY-----LEGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 4444444444443 222336789999999999999987654544443
No 97
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=37.07 E-value=86 Score=29.74 Aligned_cols=49 Identities=20% Similarity=0.335 Sum_probs=29.0
Q ss_pred hhhhhhhhHHHHHH-HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 041877 78 IAIWFQNRRARWKT-KQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAEL 126 (254)
Q Consensus 78 V~vWFQNRRak~Kr-~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 126 (254)
++|||+|-|+-.+- .+..++.+.+.+.+..++..+..-..+.++|..++
T Consensus 16 CKiWi~dN~~Sv~~He~GkrHke~V~Kritdi~rks~~kekeekKls~~l 65 (336)
T KOG0150|consen 16 CKIWIKDNPASVRFHERGKRHKENVAKRITDIHRKSLKKEKEEKKLSKEL 65 (336)
T ss_pred hhhhhcCChHHHHhHhhhhHHHHHHHHHHHHHHHhhHHHHHHHHhhhhHH
Confidence 68999998887664 23444556666666666554444444444444433
No 98
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=36.89 E-value=1.3e+02 Score=27.42 Aligned_cols=45 Identities=27% Similarity=0.414 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhh
Q 041877 86 RARWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLK 130 (254)
Q Consensus 86 Rak~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 130 (254)
|-|.|-..++.+...++..+..|+.|.+.|+++|.+|=..+.-|.
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylq 134 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQ 134 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455556667777777888888888888888888888876665543
No 99
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=36.88 E-value=1.5e+02 Score=27.21 Aligned_cols=32 Identities=38% Similarity=0.592 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 041877 94 LEKDYEVLKKQFEALKADNDSLQAQNKKLHAE 125 (254)
Q Consensus 94 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e 125 (254)
+..+.+.|..+.+.|++.+..|..+|..|..+
T Consensus 102 L~een~~L~~en~~Lr~~n~~L~~~n~el~~~ 133 (292)
T KOG4005|consen 102 LTEENEILQNENDSLRAINESLLAKNHELDSE 133 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHH
Confidence 44444444444444444444444444444333
No 100
>PF08961 DUF1875: Domain of unknown function (DUF1875); InterPro: IPR015056 MIT can be found in the Nuclear receptor-binding factor 2, it has no known function. ; PDB: 2CRB_A.
Probab=36.75 E-value=11 Score=33.87 Aligned_cols=35 Identities=34% Similarity=0.440 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhh
Q 041877 95 EKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSL 129 (254)
Q Consensus 95 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 129 (254)
...+..|+...+.|.++|..|+.||++|.+|...|
T Consensus 128 ~T~I~dLrrlVe~L~aeNErLr~EnkqL~ae~arL 162 (243)
T PF08961_consen 128 ATKIADLRRLVEFLLAENERLRRENKQLKAENARL 162 (243)
T ss_dssp -----------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33456677888888888888888888888887766
No 101
>PRK14127 cell division protein GpsB; Provisional
Probab=36.72 E-value=77 Score=25.41 Aligned_cols=37 Identities=24% Similarity=0.377 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhccC
Q 041877 97 DYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNKD 133 (254)
Q Consensus 97 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 133 (254)
+....-..|+.+..++..|+.++.+|+.++..++...
T Consensus 31 FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~ 67 (109)
T PRK14127 31 FLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQV 67 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3344444556666666666666666666666655543
No 102
>PF13518 HTH_28: Helix-turn-helix domain
Probab=36.68 E-value=38 Score=22.00 Aligned_cols=22 Identities=18% Similarity=0.508 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCChhhhhhhhhh
Q 041877 63 RKLQLARALGLQPRQIAIWFQN 84 (254)
Q Consensus 63 ~r~~LA~~LgL~~rqV~vWFQN 84 (254)
...++|+.+|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3557899999999999999754
No 103
>smart00340 HALZ homeobox associated leucin zipper.
Probab=36.29 E-value=72 Score=21.48 Aligned_cols=31 Identities=29% Similarity=0.387 Sum_probs=25.6
Q ss_pred HHHHHHHhhhHHHHHHHHHHHHHHHhhhccC
Q 041877 103 KQFEALKADNDSLQAQNKKLHAELVSLKNKD 133 (254)
Q Consensus 103 ~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 133 (254)
...+.|+.=-++|..||.+|+.|+.+|+.-.
T Consensus 5 vdCe~LKrcce~LteeNrRL~ke~~eLralk 35 (44)
T smart00340 5 VDCELLKRCCESLTEENRRLQKEVQELRALK 35 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3467788888899999999999999988643
No 104
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=35.37 E-value=66 Score=32.77 Aligned_cols=48 Identities=27% Similarity=0.239 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhccCCC
Q 041877 88 RWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNKDSN 135 (254)
Q Consensus 88 k~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~ 135 (254)
|..-..++....++-++.+.|+.||.+|+.+...|..|...+|-..+.
T Consensus 301 KEy~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~En~~~kvpsp~ 348 (655)
T KOG4343|consen 301 KEYMLGLEARLQALLSENEQLKKENATLKRQLDELVSENQRLKVPSPK 348 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCcccccCCCc
Confidence 333455667778888999999999999999999999998887765544
No 105
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=35.08 E-value=78 Score=35.48 Aligned_cols=56 Identities=18% Similarity=0.191 Sum_probs=50.2
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHH
Q 041877 38 KKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQ 93 (254)
Q Consensus 38 R~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~ 93 (254)
+..+-.+++..|-+.|-.+.-|+...+..|......+.+++.+||+|-|.|.++..
T Consensus 709 ~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 709 RLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 33455599999999999999999999999999999999999999999999988765
No 106
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=34.74 E-value=1.1e+02 Score=24.09 Aligned_cols=36 Identities=36% Similarity=0.453 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhc
Q 041877 96 KDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKN 131 (254)
Q Consensus 96 ~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 131 (254)
..+..++++++.++.++..++.+|..|..++..|++
T Consensus 27 ~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 27 LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 356667777777777777777777777777777765
No 107
>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=34.70 E-value=31 Score=24.32 Aligned_cols=26 Identities=23% Similarity=0.576 Sum_probs=21.1
Q ss_pred HHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 64 KLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
..+||+.||++.+.|..|-+ |-+|..
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 56899999999999999964 555554
No 108
>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=34.69 E-value=45 Score=23.16 Aligned_cols=34 Identities=26% Similarity=0.300 Sum_probs=25.6
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhh
Q 041877 44 EQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIW 81 (254)
Q Consensus 44 ~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vW 81 (254)
.|+..|+-.+. ....... +||..+|++++.|+.-
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHH
Confidence 47788888888 6666554 8999999999887653
No 109
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=34.67 E-value=1.6e+02 Score=23.64 Aligned_cols=35 Identities=29% Similarity=0.419 Sum_probs=22.1
Q ss_pred hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 041877 75 PRQIAIWFQNRRARWKTKQLEKDYEVLKKQFEALKADN 112 (254)
Q Consensus 75 ~rqV~vWFQNRRak~Kr~~~~~~~~~lk~~~~~l~~e~ 112 (254)
-||...||-.+|.-.. ..+....++..++.++.|-
T Consensus 17 aRq~e~~FlqKr~~LS---~~kpe~~lkEEi~eLK~El 51 (106)
T PF11594_consen 17 ARQMEAFFLQKRFELS---AYKPEQVLKEEINELKEEL 51 (106)
T ss_pred HHHHHHHHHHHHHHHH---hcCHHHHHHHHHHHHHHHH
Confidence 3677899999998773 2334445555566665443
No 110
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=34.53 E-value=7.8 Score=40.57 Aligned_cols=57 Identities=18% Similarity=0.298 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHH
Q 041877 38 KKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQL 94 (254)
Q Consensus 38 R~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~ 94 (254)
+.....++-..|...+..+..+...+-..++..|-..+..|.+||++|+...+...+
T Consensus 630 ~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 630 RSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred cCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcc
Confidence 334555556667788887777776666566666888899999999999998887553
No 111
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=34.44 E-value=2.1e+02 Score=22.08 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=31.8
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCC-Chhhhhhhhhh
Q 041877 38 KKRLNLEQVKALEKSFELGNKLEPERKLQLARALGL-QPRQIAIWFQN 84 (254)
Q Consensus 38 R~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL-~~rqV~vWFQN 84 (254)
+++|+.+....+=+.+....+ ...+||+.+|+ ...++..|-+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 678999976655555544443 56789999996 99999988653
No 112
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=34.39 E-value=1.5e+02 Score=23.58 Aligned_cols=44 Identities=27% Similarity=0.357 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhccCCC
Q 041877 92 KQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNKDSN 135 (254)
Q Consensus 92 ~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~ 135 (254)
.+.+.....+-.++..|+.....+-.||..|+-|+..|+.....
T Consensus 11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~ 54 (107)
T PF06156_consen 11 DQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEE 54 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677888888999999999999999999999999999887643
No 113
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=33.97 E-value=33 Score=22.39 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=17.1
Q ss_pred HHHHHHHHHhCCChhhhhhhhh
Q 041877 62 ERKLQLARALGLQPRQIAIWFQ 83 (254)
Q Consensus 62 ~~r~~LA~~LgL~~rqV~vWFQ 83 (254)
....++|+.+|++...|..|.+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3467899999999999999975
No 114
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.91 E-value=56 Score=25.49 Aligned_cols=39 Identities=23% Similarity=0.271 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhh
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIA 79 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~ 79 (254)
++++|...-...|+.+--.+.....++|..|++++--|+
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 567777766666666666666778899999999885443
No 115
>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=33.51 E-value=44 Score=21.83 Aligned_cols=21 Identities=19% Similarity=0.355 Sum_probs=18.7
Q ss_pred HHHHHhCCChhhhhhhhhhhH
Q 041877 66 QLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 66 ~LA~~LgL~~rqV~vWFQNRR 86 (254)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 116
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=33.42 E-value=56 Score=27.29 Aligned_cols=31 Identities=10% Similarity=0.154 Sum_probs=23.4
Q ss_pred HHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 61 PERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 61 ~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
.....++|..+|+++..|+.|+..-|.+.|.
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3446789999999999999998655544443
No 117
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=33.35 E-value=1.3e+02 Score=24.15 Aligned_cols=44 Identities=14% Similarity=0.274 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
++..+..+|...| .. ..-.+||..+|+++..|+.+...-|.+.|
T Consensus 113 L~~~~r~il~l~~--~g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 113 MTERDRTVLLLRF--SG----YSYKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred CCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555555555555 22 23567899999999999988754444433
No 118
>PRK00118 putative DNA-binding protein; Validated
Probab=33.34 E-value=2.4e+02 Score=22.25 Aligned_cols=47 Identities=9% Similarity=-0.012 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
.++..|..++...|... ....+||+.+|+++.-|..|...-|.+.|.
T Consensus 17 ~L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35666777776655443 235679999999999999998755555444
No 119
>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=33.06 E-value=68 Score=25.28 Aligned_cols=45 Identities=16% Similarity=0.118 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
++..+..+|...|- ......++|..+|+++..|+.+...-|.+.|
T Consensus 114 L~~~~r~il~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRF-----EGKSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34444445444332 2223567899999999999987754444433
No 120
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=32.67 E-value=2.2e+02 Score=21.62 Aligned_cols=37 Identities=14% Similarity=0.294 Sum_probs=26.7
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhH
Q 041877 37 KKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 37 kR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
.++.|+..++..|.... ..+.+|++..+|+-++....
T Consensus 35 g~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 35 GYRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred CceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHcCc
Confidence 34569999998885543 24567888888888886543
No 121
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=32.11 E-value=38 Score=23.49 Aligned_cols=21 Identities=19% Similarity=0.434 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 041877 64 KLQLARALGLQPRQIAIWFQN 84 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQN 84 (254)
..++|+.+|++.+.|+.|=+.
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999643
No 122
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=31.60 E-value=2.5e+02 Score=21.92 Aligned_cols=38 Identities=18% Similarity=0.186 Sum_probs=28.7
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHH
Q 041877 37 KKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRA 87 (254)
Q Consensus 37 kR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRa 87 (254)
..+.|+.+++..|+ .....+.+|++...|+..+.....
T Consensus 35 gyR~Y~~~~i~~l~-------------~I~~lr~~G~sl~eI~~~l~~~~~ 72 (123)
T cd04770 35 GYRLYGEADLARLR-------------FIRRAQALGFSLAEIRELLSLRDD 72 (123)
T ss_pred CCccCCHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHHhhhc
Confidence 45679999999883 344578899999999988876543
No 123
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=31.05 E-value=73 Score=26.17 Aligned_cols=46 Identities=11% Similarity=0.098 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
++..+..+++..|- ....-.++|..+|+++..|+.+...-|.+.|.
T Consensus 137 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 137 LPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55555555554332 23345789999999999999988655554443
No 124
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=30.94 E-value=1.2e+02 Score=25.83 Aligned_cols=28 Identities=21% Similarity=0.195 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 63 RKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 63 ~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
.-.++|..+|+++..|+++...-|.+.+
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 198 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLK 198 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4578999999999999888755444444
No 125
>PRK10884 SH3 domain-containing protein; Provisional
Probab=30.93 E-value=1.7e+02 Score=25.80 Aligned_cols=30 Identities=20% Similarity=0.117 Sum_probs=13.4
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHHHHHhhh
Q 041877 101 LKKQFEALKADNDSLQAQNKKLHAELVSLK 130 (254)
Q Consensus 101 lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 130 (254)
++.+++.|+.+...++.+++.|.+++..++
T Consensus 137 L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~ 166 (206)
T PRK10884 137 LKEENQKLKNQLIVAQKKVDAANLQLDDKQ 166 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444444444444444444444443
No 126
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=30.54 E-value=1.6e+02 Score=28.30 Aligned_cols=47 Identities=30% Similarity=0.395 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhc
Q 041877 85 RRARWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKN 131 (254)
Q Consensus 85 RRak~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 131 (254)
+|.+.+-.+...+.+.+|+..|.++.....|.++.+.|+.+...|+.
T Consensus 221 ~r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~ 267 (365)
T KOG2391|consen 221 RRREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQK 267 (365)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHh
Confidence 34455555556666667777777666666666666666666555443
No 127
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=30.48 E-value=1.7e+02 Score=21.28 Aligned_cols=30 Identities=23% Similarity=0.376 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 041877 93 QLEKDYEVLKKQFEALKADNDSLQAQNKKL 122 (254)
Q Consensus 93 ~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l 122 (254)
....+...++.+.+.+..+++.|+.|...|
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l 57 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAEL 57 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555666666666666655554443
No 128
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=30.46 E-value=2e+02 Score=20.36 Aligned_cols=33 Identities=15% Similarity=0.412 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 041877 94 LEKDYEVLKKQFEALKADNDSLQAQNKKLHAEL 126 (254)
Q Consensus 94 ~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~ 126 (254)
++.+...+...+..++.++..+..+.+.+...+
T Consensus 5 lEn~~~~~~~~i~tvk~en~~i~~~ve~i~env 37 (55)
T PF05377_consen 5 LENELPRIESSINTVKKENEEISESVEKIEENV 37 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444455555555566666655555555554443
No 129
>PRK10884 SH3 domain-containing protein; Provisional
Probab=30.44 E-value=1.6e+02 Score=25.98 Aligned_cols=34 Identities=15% Similarity=0.135 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhh
Q 041877 97 DYEVLKKQFEALKADNDSLQAQNKKLHAELVSLK 130 (254)
Q Consensus 97 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk 130 (254)
..+..+..+..|+.+|..|+.+...++.++..++
T Consensus 126 ~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~ 159 (206)
T PRK10884 126 KVAQSDSVINGLKEENQKLKNQLIVAQKKVDAAN 159 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344445555555555555555555555554443
No 130
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=30.27 E-value=1.6e+02 Score=20.85 Aligned_cols=33 Identities=24% Similarity=0.467 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhh
Q 041877 97 DYEVLKKQFEALKADNDSLQAQNKKLHAELVSL 129 (254)
Q Consensus 97 ~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 129 (254)
.+..++.++..+..+...++.+++.|+.++..+
T Consensus 18 ~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 18 RYYQLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455666667777777777777777777777666
No 131
>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=30.27 E-value=39 Score=22.30 Aligned_cols=23 Identities=26% Similarity=0.371 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChhhhhhhhhhhH
Q 041877 64 KLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
..+||+.+|+++..|..|..+++
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 47899999999999999998854
No 132
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=30.07 E-value=59 Score=26.17 Aligned_cols=28 Identities=11% Similarity=0.105 Sum_probs=21.8
Q ss_pred HHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 64 KLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
-.++|..+|+++..|+.....-|.+.|.
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4689999999999999988655555444
No 133
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=30.05 E-value=1.7e+02 Score=21.21 Aligned_cols=39 Identities=18% Similarity=0.326 Sum_probs=19.1
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 041877 78 IAIWFQNRRARWKTKQLEKDYEVLKKQFEALKADNDSLQ 116 (254)
Q Consensus 78 V~vWFQNRRak~Kr~~~~~~~~~lk~~~~~l~~e~~~l~ 116 (254)
|..+++.+.........+.+.+.++.+.+.|+.+-..+.
T Consensus 20 v~~~~~~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 20 VSAQHQTRQLNNELQKLQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 333444444444444455555555555555555555443
No 134
>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=29.85 E-value=50 Score=20.58 Aligned_cols=24 Identities=21% Similarity=0.516 Sum_probs=20.1
Q ss_pred HHHHHHHhCCChhhhhhhhhhhHH
Q 041877 64 KLQLARALGLQPRQIAIWFQNRRA 87 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQNRRa 87 (254)
..++|+.||++.+.|..|.++.+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999876543
No 135
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=29.79 E-value=1.1e+02 Score=24.65 Aligned_cols=30 Identities=33% Similarity=0.521 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Q 041877 95 EKDYEVLKKQFEALKADNDSLQAQNKKLHA 124 (254)
Q Consensus 95 ~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~ 124 (254)
+.+.+.||.++..|.+.+..|++||.-|+.
T Consensus 66 REEVe~Lk~qI~eL~er~~~Le~EN~lLk~ 95 (123)
T KOG4797|consen 66 REEVEVLKEQIRELEERNSALERENSLLKT 95 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456778888888888888888888766653
No 136
>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=29.56 E-value=1.5e+02 Score=18.95 Aligned_cols=36 Identities=14% Similarity=0.257 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 041877 42 NLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQ 83 (254)
Q Consensus 42 t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQ 83 (254)
+..+...+...+. . ....++|+.++++++.|..|..
T Consensus 2 ~~~e~~i~~~~~~--~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE--G----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHH
Confidence 4455556655432 1 2457889999999999998875
No 137
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=29.37 E-value=1.8e+02 Score=26.61 Aligned_cols=17 Identities=29% Similarity=0.569 Sum_probs=6.2
Q ss_pred HHHHHHHHHhhhHHHHH
Q 041877 101 LKKQFEALKADNDSLQA 117 (254)
Q Consensus 101 lk~~~~~l~~e~~~l~~ 117 (254)
+|.+++.+..++..|..
T Consensus 140 ~kekl~E~~~EkeeL~~ 156 (290)
T COG4026 140 LKEKLEELQKEKEELLK 156 (290)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33333333333333333
No 138
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=29.28 E-value=1.3e+02 Score=30.06 Aligned_cols=44 Identities=20% Similarity=0.377 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhccC
Q 041877 90 KTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNKD 133 (254)
Q Consensus 90 Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~ 133 (254)
|...++++++.++++.+.+......++...+.|++|+..|+...
T Consensus 77 kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 77 TAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 33445555555555555444444455555555566666655543
No 139
>PF13551 HTH_29: Winged helix-turn helix
Probab=29.18 E-value=1.6e+02 Score=21.87 Aligned_cols=44 Identities=20% Similarity=0.193 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHhhcCCCC-----CHHHHHH-H-HHHh--CCChhhhhhhhh
Q 041877 40 RLNLEQVKALEKSFELGNKL-----EPERKLQ-L-ARAL--GLQPRQIAIWFQ 83 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp-----~~~~r~~-L-A~~L--gL~~rqV~vWFQ 83 (254)
+++.++...|...+...+.- ......+ | .... .+++..|..|+.
T Consensus 57 ~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 57 RLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 39999999999999987632 2232222 3 2222 467777777764
No 140
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.79 E-value=1.2e+02 Score=25.24 Aligned_cols=44 Identities=20% Similarity=0.128 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARW 89 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~ 89 (254)
++..+..++...|-. ...-.+||..+|+++..|+.+...-|.+.
T Consensus 140 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 140 LPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQHRALARL 183 (189)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 556666666654433 23467899999999999998875433333
No 141
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.62 E-value=98 Score=25.54 Aligned_cols=46 Identities=11% Similarity=0.016 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
++..+..+|...|-. ...-.+||..||++...|+.++..-|.+.|.
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 132 LPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 555555555554332 2335689999999999999988655555443
No 142
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=28.52 E-value=91 Score=29.96 Aligned_cols=19 Identities=32% Similarity=0.417 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHhhhHHH
Q 041877 97 DYEVLKKQFEALKADNDSL 115 (254)
Q Consensus 97 ~~~~lk~~~~~l~~e~~~l 115 (254)
+...||+++++|+.+...|
T Consensus 40 EN~~LKkEN~~Lk~eVerL 58 (420)
T PF07407_consen 40 ENHSLKKENNDLKIEVERL 58 (420)
T ss_pred HhHHHHHHHHHHHHHHHHH
Confidence 3344444444444444333
No 143
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=28.01 E-value=1.5e+02 Score=23.59 Aligned_cols=43 Identities=21% Similarity=0.155 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak 88 (254)
++..+..++...| .....-.++|..+|+++..|.++...-|.+
T Consensus 112 L~~~~r~v~~l~~-----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 112 LPERQRELLQLRY-----QRGVSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred CCHHHHHHHHHHH-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5555555555533 223346789999999999999876543333
No 144
>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=27.86 E-value=45 Score=23.37 Aligned_cols=21 Identities=19% Similarity=0.420 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 041877 64 KLQLARALGLQPRQIAIWFQN 84 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQN 84 (254)
..++|+.+|++++.++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 145
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.72 E-value=3.1e+02 Score=21.69 Aligned_cols=37 Identities=24% Similarity=0.262 Sum_probs=29.0
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhH
Q 041877 37 KKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 37 kR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
..+.|+.+++..|. .....+.+|++-..|+-++....
T Consensus 35 gyR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~ 71 (126)
T cd04783 35 GYRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLELDD 71 (126)
T ss_pred CCeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhccc
Confidence 34569999998884 45567899999999999987654
No 146
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. 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; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=27.56 E-value=46 Score=21.32 Aligned_cols=18 Identities=28% Similarity=0.549 Sum_probs=15.0
Q ss_pred HHHHHHhCCChhhhhhhh
Q 041877 65 LQLARALGLQPRQIAIWF 82 (254)
Q Consensus 65 ~~LA~~LgL~~rqV~vWF 82 (254)
-++|+.+|++.+.|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 478999999999999984
No 147
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=27.55 E-value=87 Score=25.96 Aligned_cols=28 Identities=7% Similarity=0.196 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 63 RKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 63 ~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
.-.+||..+|++...|+.+...-|.+.|
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALR 173 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 3568999999999999998754444433
No 148
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=27.32 E-value=1.6e+02 Score=23.51 Aligned_cols=46 Identities=20% Similarity=0.181 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
++..+..+|...|-. ...-.++|..+|+++..|+.+-..-|.+.|+
T Consensus 111 L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 445555555544421 2335688999999999999887655554443
No 149
>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=27.16 E-value=49 Score=23.07 Aligned_cols=21 Identities=10% Similarity=0.398 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChhhhhhhhhh
Q 041877 64 KLQLARALGLQPRQIAIWFQN 84 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQN 84 (254)
..++|+.+|++++.++.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 150
>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=26.96 E-value=52 Score=20.23 Aligned_cols=23 Identities=26% Similarity=0.346 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChhhhhhhhhhhH
Q 041877 64 KLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
..++|+.+|+++..|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45889999999999999987764
No 151
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=26.94 E-value=2.4e+02 Score=22.62 Aligned_cols=43 Identities=30% Similarity=0.355 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhccCC
Q 041877 92 KQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNKDS 134 (254)
Q Consensus 92 ~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~ 134 (254)
.+.+.....+-.++..|+.....+-.||..|+-|+..|+....
T Consensus 11 ~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~ 53 (110)
T PRK13169 11 DDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLE 53 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567778888889999999999999999999999999888654
No 152
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=26.85 E-value=3.2e+02 Score=21.63 Aligned_cols=37 Identities=27% Similarity=0.264 Sum_probs=28.1
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhH
Q 041877 37 KKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 37 kR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
..+.|+..++..| .....++.+|++...|+..+....
T Consensus 34 g~R~Y~~~~l~~l-------------~~I~~l~~~G~sl~eI~~~l~~~~ 70 (124)
T TIGR02051 34 GYRRYPEETVKRL-------------RFIKRAQELGFSLEEIGGLLGLVD 70 (124)
T ss_pred CCEeECHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHhccc
Confidence 4556999998888 344557899999999999886543
No 153
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=26.49 E-value=1.8e+02 Score=25.01 Aligned_cols=56 Identities=29% Similarity=0.406 Sum_probs=24.3
Q ss_pred CChhhhhhhhhhhHHHHH-HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHh
Q 041877 73 LQPRQIAIWFQNRRARWK-TKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVS 128 (254)
Q Consensus 73 L~~rqV~vWFQNRRak~K-r~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~ 128 (254)
|+-..|-...|+-..... -.....+...++.+...|...+..|..++..|..++..
T Consensus 80 ltl~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~ 136 (161)
T TIGR02894 80 LTLQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQRLST 136 (161)
T ss_pred CCHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555544332111 12233344444444555555555555555554444433
No 154
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=26.48 E-value=1e+02 Score=26.89 Aligned_cols=46 Identities=13% Similarity=0.186 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
++..+..++...|. ....-.++|..+|+++..|+.+...-|.+.|+
T Consensus 185 L~~~~r~vl~l~~~-----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQ-----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhc-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45555555555442 22346789999999999999988766655554
No 155
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=26.30 E-value=2e+02 Score=22.82 Aligned_cols=43 Identities=14% Similarity=0.047 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak 88 (254)
++..+..++...|-. ...-.++|..||+++..|++....-|.+
T Consensus 107 Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 107 LPARQREAFLLRYWE-----DMDVAETAAAMGCSEGSVKTHCSRATHA 149 (161)
T ss_pred CCHHHHHHHHHHHHh-----cCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 555565555554322 1225789999999999999876543333
No 156
>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=25.26 E-value=1.1e+02 Score=26.32 Aligned_cols=45 Identities=11% Similarity=0.126 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
++..+..+|...|-.. ....++|..+|++...|+.+...-+.+.|
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 5666777777766322 24578999999999999887654444433
No 157
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=25.05 E-value=1.4e+02 Score=29.78 Aligned_cols=28 Identities=25% Similarity=0.265 Sum_probs=14.6
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARA 70 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~ 70 (254)
.++++++..|.- ..-.|....|.-+|+.
T Consensus 41 ~ltpee~kalGi---egDTP~DTlrTlva~~ 68 (472)
T TIGR03752 41 ELSPEELKALGI---EGDTPADTLRTLVAEV 68 (472)
T ss_pred cCCcchhHhcCC---CCCCccchHHHHHHHH
Confidence 577777666543 2334555545444443
No 158
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=24.93 E-value=1.8e+02 Score=23.80 Aligned_cols=39 Identities=21% Similarity=0.068 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhh
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQN 84 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQN 84 (254)
++..+..+|...|-. ...-.+||..+|+++..|+.+...
T Consensus 101 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~R 139 (170)
T TIGR02959 101 LPDEYREAIRLTELE-----GLSQQEIAEKLGLSLSGAKSRVQR 139 (170)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 555555555554422 223568899999999999887643
No 159
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=24.86 E-value=1.2e+02 Score=22.87 Aligned_cols=27 Identities=30% Similarity=0.428 Sum_probs=19.5
Q ss_pred HHHHhhhHHHHHHHHHHHHHHHhhhcc
Q 041877 106 EALKADNDSLQAQNKKLHAELVSLKNK 132 (254)
Q Consensus 106 ~~l~~e~~~l~~e~~~l~~e~~~lk~~ 132 (254)
.++..+|..|+.+..+|.+|+..++..
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~~~ 29 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNKRE 29 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 456677778888888888887776553
No 160
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=24.77 E-value=1.4e+02 Score=27.85 Aligned_cols=50 Identities=24% Similarity=0.282 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
+++..+..+|+..|.... .......+||..+|++...|+.+...-+.+.|
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr 311 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLR 311 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 478888888887774322 23445688999999999999998765444444
No 161
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=24.75 E-value=1.5e+02 Score=25.77 Aligned_cols=49 Identities=24% Similarity=0.249 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
++..+..++...|.. .+.....-.++|..+|+++..|+.+...-|.+.|
T Consensus 179 Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr 227 (234)
T PRK08301 179 LSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLK 227 (234)
T ss_pred CCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 566666666665521 1123334678999999999999887654444433
No 162
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=24.72 E-value=3.7e+02 Score=21.54 Aligned_cols=73 Identities=11% Similarity=0.125 Sum_probs=41.4
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 041877 37 KKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDYEVLKKQFEALKADNDSLQ 116 (254)
Q Consensus 37 kR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~~~~~~lk~~~~~l~~e~~~l~ 116 (254)
..+.|+.+++..| ......+.+|++-.+|+-++.......... ....+.++.+.+.+..+-..++
T Consensus 35 gyR~Y~~~~~~~l-------------~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~--~~~~~~l~~~~~~l~~~i~~l~ 99 (133)
T cd04787 35 GYRLYSEKDLSRL-------------RFILSARQLGFSLKDIKEILSHADQGESPC--PMVRRLIEQRLAETERRIKELL 99 (133)
T ss_pred CeeeCCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHhhhccCCCcH--HHHHHHHHHHHHHHHHHHHHHH
Confidence 3456999998888 344557899999999999987543211110 1112334444444544444444
Q ss_pred HHHHHHHH
Q 041877 117 AQNKKLHA 124 (254)
Q Consensus 117 ~e~~~l~~ 124 (254)
.-...|..
T Consensus 100 ~~~~~l~~ 107 (133)
T cd04787 100 KLRDRMQQ 107 (133)
T ss_pred HHHHHHHH
Confidence 44444433
No 163
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=24.72 E-value=1.5e+02 Score=26.64 Aligned_cols=16 Identities=31% Similarity=0.464 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHHHHh
Q 041877 95 EKDYEVLKKQFEALKA 110 (254)
Q Consensus 95 ~~~~~~lk~~~~~l~~ 110 (254)
.++.+.|+++...++.
T Consensus 75 ~~en~~L~~e~~~l~~ 90 (276)
T PRK13922 75 REENEELKKELLELES 90 (276)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3344444444444443
No 164
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=24.67 E-value=1.3e+02 Score=25.14 Aligned_cols=46 Identities=20% Similarity=0.280 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
+++.+..++.-.|-. .....+||..+|++...|+...+.-|.+.|+
T Consensus 132 L~~~~r~i~~l~~~~-----g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 132 LEKLDREIFIRRYLL-----GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 555555555543321 2335688999999999988876544444333
No 165
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=24.45 E-value=2e+02 Score=23.58 Aligned_cols=27 Identities=22% Similarity=0.229 Sum_probs=21.0
Q ss_pred HHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 64 KLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
-.++|..||+++..|++....-|.+.|
T Consensus 153 ~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 153 VEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 568899999999999998765444443
No 166
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.29 E-value=2.3e+02 Score=23.53 Aligned_cols=46 Identities=7% Similarity=0.151 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
++..+..+|+..|- ....-.++|..+|+++..|++-...-|.+.|.
T Consensus 132 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYY-----HEKSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 55555555555432 22235688999999999999877544444443
No 167
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=24.15 E-value=1.8e+02 Score=21.60 Aligned_cols=43 Identities=14% Similarity=0.141 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHhhcC-----CCCCHHHHHHHHHHhCCChhhhhhhhh
Q 041877 41 LNLEQVKALEKSFELG-----NKLEPERKLQLARALGLQPRQIAIWFQ 83 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~-----~yp~~~~r~~LA~~LgL~~rqV~vWFQ 83 (254)
++.+|+..|...|... .+.+..+..++-+.+|+++..|...|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 6788999999998753 356666666666667887777776663
No 168
>PRK10403 transcriptional regulator NarP; Provisional
Probab=24.14 E-value=1.2e+02 Score=24.48 Aligned_cols=45 Identities=13% Similarity=0.178 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
.+|..+..+|+....- ..+.+||+.++++++-|++..++=|.|..
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 4788888888765543 34678999999999999998876665543
No 169
>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=24.10 E-value=59 Score=21.18 Aligned_cols=23 Identities=22% Similarity=0.120 Sum_probs=20.2
Q ss_pred HHHHHHHhCCChhhhhhhhhhhH
Q 041877 64 KLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56899999999999999997764
No 170
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.07 E-value=4e+02 Score=21.74 Aligned_cols=66 Identities=9% Similarity=0.141 Sum_probs=35.3
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHH-HHHHHHHHHHHHHHHHHHHHHHhhhHHH
Q 041877 37 KKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRA-RWKTKQLEKDYEVLKKQFEALKADNDSL 115 (254)
Q Consensus 37 kR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRa-k~Kr~~~~~~~~~lk~~~~~l~~e~~~l 115 (254)
..+.|+..++..|... ...+.+|++-..|+-++.+... ...........+.+..+.+.+...-..+
T Consensus 34 g~R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~i~~Le~~l~~L 100 (134)
T cd04779 34 NYRYYDETALDRLQLI-------------EHLKGQRLSLAEIKDQLEEVQRSDKEQREVAQEVQLVCDQIDGLEHRLKQL 100 (134)
T ss_pred CCeeECHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556999998887432 2246677777777777755442 1122223333444444444444433333
No 171
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=23.94 E-value=2.1e+02 Score=23.93 Aligned_cols=30 Identities=13% Similarity=0.148 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 61 PERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 61 ~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
...-.+||..+|+++..|++-...-|.+.|
T Consensus 170 ~~s~~EIA~~lgis~~tV~~~l~rar~~Lr 199 (208)
T PRK08295 170 GKSYQEIAEELNRHVKSIDNALQRVKRKLE 199 (208)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 344578999999999999876654444433
No 172
>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.
Probab=23.86 E-value=4.5e+02 Score=22.28 Aligned_cols=72 Identities=21% Similarity=0.229 Sum_probs=33.5
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHHHHHH----HHHHHHHHHHhhhHHHHHHHH
Q 041877 45 QVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDYE----VLKKQFEALKADNDSLQAQNK 120 (254)
Q Consensus 45 Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~~~~~----~lk~~~~~l~~e~~~l~~e~~ 120 (254)
-|..|+.++..+.-..... ++.+ ...-+.=.+.+|.|..+++.+..+. .+......+......++.++.
T Consensus 34 vLE~Le~~~~~n~~~~~e~--~~L~-----~d~e~L~~q~~~ek~~r~~~e~~l~~~Ed~~~~e~k~L~~~v~~Le~e~r 106 (158)
T PF09744_consen 34 VLELLESLASRNQEHEVEL--ELLR-----EDNEQLETQYEREKELRKQAEEELLELEDQWRQERKDLQSQVEQLEEENR 106 (158)
T ss_pred HHHHHHHHHHhhhhhhhHH--HHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777777766333221 1111 1112223345566666655555444 344444444444444455554
Q ss_pred HHH
Q 041877 121 KLH 123 (254)
Q Consensus 121 ~l~ 123 (254)
.|.
T Consensus 107 ~L~ 109 (158)
T PF09744_consen 107 QLE 109 (158)
T ss_pred HHH
Confidence 444
No 173
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=23.71 E-value=1.1e+02 Score=24.89 Aligned_cols=29 Identities=21% Similarity=0.145 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 63 RKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 63 ~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
...++|..+|+++..|+.|...-|.+.|+
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999987654444443
No 174
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=23.46 E-value=2.2e+02 Score=21.45 Aligned_cols=22 Identities=23% Similarity=0.478 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHhhhHHHHHHH
Q 041877 98 YEVLKKQFEALKADNDSLQAQN 119 (254)
Q Consensus 98 ~~~lk~~~~~l~~e~~~l~~e~ 119 (254)
...++.+.+.+..++..|+.|.
T Consensus 44 l~~l~~~~~~l~~e~~~L~lE~ 65 (97)
T PF04999_consen 44 LQQLEKEIDQLQEENERLRLEI 65 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444443
No 175
>PRK14127 cell division protein GpsB; Provisional
Probab=23.28 E-value=3.3e+02 Score=21.78 Aligned_cols=51 Identities=25% Similarity=0.462 Sum_probs=38.5
Q ss_pred CCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhc
Q 041877 72 GLQPRQIAIWFQNRRARWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKN 131 (254)
Q Consensus 72 gL~~rqV~vWFQNRRak~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 131 (254)
|..+.+|.-+.. ....+++.+..++..|+.++..++.+...++..+.....
T Consensus 22 GYd~~EVD~FLd---------~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~~~~ 72 (109)
T PRK14127 22 GYDQDEVDKFLD---------DVIKDYEAFQKEIEELQQENARLKAQVDELTKQVSVGAS 72 (109)
T ss_pred CCCHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccc
Confidence 666666766653 556688888888889999999998888888887775543
No 176
>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=23.01 E-value=72 Score=21.98 Aligned_cols=20 Identities=25% Similarity=0.481 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChhhhhhhhh
Q 041877 64 KLQLARALGLQPRQIAIWFQ 83 (254)
Q Consensus 64 r~~LA~~LgL~~rqV~vWFQ 83 (254)
..++|+.+|+++..|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999985
No 177
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=22.71 E-value=96 Score=25.26 Aligned_cols=33 Identities=15% Similarity=0.181 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 59 LEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 59 p~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
.....-.++|..+|+++..|+..+..-|.+.|+
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344456789999999999999988655555444
No 178
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=22.67 E-value=4.5e+02 Score=21.79 Aligned_cols=46 Identities=15% Similarity=0.093 Sum_probs=33.9
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 39 KRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 39 ~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
.-++..|..+|+..+ .. ....++|..+|++..-|..+-..-|.+.+
T Consensus 5 ~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 5 TFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred CCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 457888999887742 22 24678999999999999988765555544
No 179
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=22.31 E-value=1.4e+02 Score=26.42 Aligned_cols=45 Identities=9% Similarity=0.124 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
++..+..+|...|-. ...-.++|..||+++..|+.|...-+.+.|
T Consensus 206 L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 206 LSDREKSIIQCTFIE-----NLSQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 566677777666532 223578999999999999988754444433
No 180
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.26 E-value=1.3e+02 Score=25.27 Aligned_cols=46 Identities=11% Similarity=0.142 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
++..+..++...|-. ...-.++|..||+++..|+.+...-|.+.|.
T Consensus 135 Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYL-----ELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 455555555544322 2235789999999999999987644444443
No 181
>PRK09480 slmA division inhibitor protein; Provisional
Probab=22.23 E-value=1.1e+02 Score=25.17 Aligned_cols=40 Identities=20% Similarity=0.243 Sum_probs=31.5
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHH
Q 041877 47 KALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRA 87 (254)
Q Consensus 47 ~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRa 87 (254)
......|...+. ......+||+..|++..-+-.+|.|+-.
T Consensus 17 ~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 17 QALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 333444655556 7788899999999999999999999764
No 182
>PF03234 CDC37_N: Cdc37 N terminal kinase binding; InterPro: IPR013855 In Saccharomyces cerevisiae (Baker's yeast), cell division control protein Cdc37 is required for the productive formation of Cdc28-cyclin complexes. Cdc37 may be a kinase targeting subunit of Hsp90 [].
Probab=22.09 E-value=3.2e+02 Score=23.69 Aligned_cols=45 Identities=24% Similarity=0.361 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhcc
Q 041877 88 RWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNK 132 (254)
Q Consensus 88 k~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~ 132 (254)
+||..++....+..+.+.+.++.+.......+.++..-+..++..
T Consensus 31 rwk~~~~~e~~~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~~~~~ 75 (177)
T PF03234_consen 31 RWKHQARHERREERKQEIEELKYERKINEKLLKRIQKLLSALDKE 75 (177)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 456666666666677777777776665555555555555544443
No 183
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=21.96 E-value=93 Score=24.89 Aligned_cols=44 Identities=14% Similarity=0.091 Sum_probs=28.7
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 041877 63 RKLQLARALGLQPRQIAIWFQNRRARWKTKQLEKDYEVLKKQFEA 107 (254)
Q Consensus 63 ~r~~LA~~LgL~~rqV~vWFQNRRak~Kr~~~~~~~~~lk~~~~~ 107 (254)
.+.+||..+|++...|..|.++++. -......+-...+.-..+.
T Consensus 20 sq~eLA~~~Gis~~~is~iE~g~~~-ps~~~l~kIa~aL~v~~~~ 63 (120)
T PRK13890 20 TKKELSERSGVSISFLSDLTTGKAN-PSLKVMEAIADALETPLPL 63 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCC-CCHHHHHHHHHHHCCCHHH
Confidence 3678999999999999999988763 3444444433333333333
No 184
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=21.93 E-value=1.8e+02 Score=23.57 Aligned_cols=45 Identities=11% Similarity=0.106 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
++..+..++...|-.. ..-.++|..||+++..|+.+...-|.+.|
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4555555555544322 33568899999999999987654444433
No 185
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=21.85 E-value=1.4e+02 Score=23.90 Aligned_cols=44 Identities=20% Similarity=0.228 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARW 89 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~ 89 (254)
.+|..+...|+-..+- ..+.+||..++++++.|+...++=|.|.
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4777777777766543 2577889999999999988776655543
No 186
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=21.64 E-value=2.3e+02 Score=24.74 Aligned_cols=51 Identities=12% Similarity=0.170 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
.++..+..+|...|....+ ....-.+||..+|++...|+.....-+.|.|.
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 3677777888887743222 23346789999999999999887655555544
No 187
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. 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 RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=21.63 E-value=1e+02 Score=25.34 Aligned_cols=30 Identities=10% Similarity=-0.019 Sum_probs=22.0
Q ss_pred HHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 61 PERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 61 ~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
...-.+||..+|+++..|+++...-|.+.|
T Consensus 154 ~~s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 154 GLSYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 344678999999999999988754444433
No 188
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.58 E-value=1.4e+02 Score=24.52 Aligned_cols=43 Identities=19% Similarity=0.227 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRAR 88 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak 88 (254)
++..+..+|...| .....-.++|..+|+++..|+.+...-|.+
T Consensus 136 L~~~~r~vl~l~~-----~~~~s~~eIA~~lgis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 136 LSPEERRVIEVLY-----YQGYTHREAAQLLGLPLGTLKTRARRALSR 178 (186)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4455555554433 222235688999999999999876543333
No 189
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=21.45 E-value=1e+02 Score=24.38 Aligned_cols=33 Identities=15% Similarity=0.128 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 58 KLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 58 yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
|.....-.++|..+|+++..|+++...-|.+.|
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELK 150 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 345556789999999999999988764444433
No 190
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=21.35 E-value=2.6e+02 Score=22.19 Aligned_cols=50 Identities=26% Similarity=0.359 Sum_probs=35.5
Q ss_pred hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Q 041877 75 PRQIAIWFQNRRARWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAE 125 (254)
Q Consensus 75 ~rqV~vWFQNRRak~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e 125 (254)
.-+.-.||... ....-.......+.++++++.+.+++..+.++...|+..
T Consensus 37 ~f~~~~~~g~~-~~~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 37 LFQYLAWFGKN-GAADVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHh-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 44555566543 233444566667788889999999999999998888777
No 191
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=21.30 E-value=3.1e+02 Score=21.58 Aligned_cols=45 Identities=13% Similarity=0.135 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
.+|..+..+|+. +... + ...++|+.++++++.|+.+.++=|.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876 3332 2 2578999999999999999876555543
No 192
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=21.29 E-value=4.8e+02 Score=23.59 Aligned_cols=55 Identities=24% Similarity=0.516 Sum_probs=27.7
Q ss_pred hhhhhhhhhhhHHHHHHHH---------HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhh
Q 041877 75 PRQIAIWFQNRRARWKTKQ---------LEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSL 129 (254)
Q Consensus 75 ~rqV~vWFQNRRak~Kr~~---------~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~l 129 (254)
...+..||+.+-...+... ...+...++..+..+..+-..++..+..|...+..+
T Consensus 186 ~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~l 249 (312)
T PF00038_consen 186 REELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASLERQLREL 249 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHH
Confidence 4678899988755544322 222333344444444444444444444444444433
No 193
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=21.20 E-value=1.3e+02 Score=23.91 Aligned_cols=25 Identities=12% Similarity=0.219 Sum_probs=21.1
Q ss_pred CHHHHHHHHHHhCCChhhhhhhhhh
Q 041877 60 EPERKLQLARALGLQPRQIAIWFQN 84 (254)
Q Consensus 60 ~~~~r~~LA~~LgL~~rqV~vWFQN 84 (254)
......+||+.+|++++.+..+|+.
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3456688999999999999999964
No 194
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=21.16 E-value=2e+02 Score=22.98 Aligned_cols=38 Identities=21% Similarity=0.205 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhh
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQ 83 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQ 83 (254)
+++.+..+|...|- ....-.++|+.||+++..|+....
T Consensus 123 L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 123 LTPKQQHVIALRFG-----QNLPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 44445455544332 223356889999999999987653
No 195
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=21.15 E-value=2.2e+02 Score=25.66 Aligned_cols=38 Identities=24% Similarity=0.205 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHhhhHHHHHHHH---HHHHHHHhhhccC
Q 041877 96 KDYEVLKKQFEALKADNDSLQAQNK---KLHAELVSLKNKD 133 (254)
Q Consensus 96 ~~~~~lk~~~~~l~~e~~~l~~e~~---~l~~e~~~lk~~~ 133 (254)
..+..++.+++.|+.++..++.+.. .+++|+..|+...
T Consensus 69 ~~~~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL 109 (276)
T PRK13922 69 ASLFDLREENEELKKELLELESRLQELEQLEAENARLRELL 109 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455677777777777777766654 5566666666543
No 196
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.08 E-value=3.9e+02 Score=20.58 Aligned_cols=37 Identities=22% Similarity=0.301 Sum_probs=27.1
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhH
Q 041877 37 KKKRLNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRR 86 (254)
Q Consensus 37 kR~r~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRR 86 (254)
..+.|+.+++..|.. ....+.+|++-.+|+..+....
T Consensus 35 gyR~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~ 71 (113)
T cd01109 35 GIRDFTEEDLEWLEF-------------IKCLRNTGMSIKDIKEYAELRR 71 (113)
T ss_pred CCccCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHHHc
Confidence 345699999888742 3446788999999988886543
No 197
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.98 E-value=2.6e+02 Score=24.56 Aligned_cols=29 Identities=7% Similarity=0.163 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCChhhhhhhhhhhHHHHHH
Q 041877 63 RKLQLARALGLQPRQIAIWFQNRRARWKT 91 (254)
Q Consensus 63 ~r~~LA~~LgL~~rqV~vWFQNRRak~Kr 91 (254)
.-.+||..||+++..|+.....-|.+.|+
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999887655544443
No 198
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=20.78 E-value=2.5e+02 Score=23.18 Aligned_cols=44 Identities=11% Similarity=0.260 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARW 89 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~ 89 (254)
++..+..++...|- ....-.++|..+|+++..|+.+...-|.+.
T Consensus 134 L~~~~r~i~~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~L 177 (182)
T PRK12537 134 LEPARRNCILHAYV-----DGCSHAEIAQRLGAPLGTVKAWIKRSLKAL 177 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCChhhHHHHHHHHHHHH
Confidence 44454444444332 222356889999999999999876444433
No 199
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=20.73 E-value=2.7e+02 Score=22.20 Aligned_cols=45 Identities=20% Similarity=0.242 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
+++.+..+|...|-. .....++|..+|++...|+.....-|.+.|
T Consensus 110 L~~~~r~v~~l~~~~-----~~s~~EIA~~lgis~~tV~~~l~ra~~~lr 154 (163)
T PRK07037 110 LPARTRYAFEMYRLH-----GETQKDIARELGVSPTLVNFMIRDALVHCR 154 (163)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 444454555443322 223578999999999999987544443333
No 200
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=20.54 E-value=3.6e+02 Score=27.58 Aligned_cols=41 Identities=29% Similarity=0.506 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhc
Q 041877 91 TKQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKN 131 (254)
Q Consensus 91 r~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~ 131 (254)
-..++.++..++..+..+..+...|+.|+.+|..++..++.
T Consensus 150 l~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r~ 190 (546)
T KOG0977|consen 150 LSELEAEINTLKRRIKALEDELKRLKAENSRLREELARARK 190 (546)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHH
Confidence 34555666666777777777777777766666666665553
No 201
>cd00131 PAX Paired Box domain
Probab=20.51 E-value=4.2e+02 Score=21.29 Aligned_cols=44 Identities=18% Similarity=0.040 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHH-HHHHhCC-------Chhhhhhhhhh
Q 041877 40 RLNLEQVKALEKSFELGNKLEPERKLQ-LARALGL-------QPRQIAIWFQN 84 (254)
Q Consensus 40 r~t~~Ql~~LE~~F~~~~yp~~~~r~~-LA~~LgL-------~~rqV~vWFQN 84 (254)
..+..+...++.....++.....+..+ |+ .-|+ +...|-.||++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~-~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLL-QEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHH-HcCCcccCCCCCHHHHHHHHHh
Confidence 456777777777777777776555544 34 3355 77777777765
No 202
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=20.46 E-value=2.2e+02 Score=25.05 Aligned_cols=45 Identities=13% Similarity=0.194 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHhCCChhhhhhhhhhhHHHHH
Q 041877 41 LNLEQVKALEKSFELGNKLEPERKLQLARALGLQPRQIAIWFQNRRARWK 90 (254)
Q Consensus 41 ~t~~Ql~~LE~~F~~~~yp~~~~r~~LA~~LgL~~rqV~vWFQNRRak~K 90 (254)
++..+..+|...|... ..-.++|..+|+++..|+.+...-+.+.|
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr 250 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLK 250 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 6677777777666432 23478999999999999888754444433
No 203
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=20.40 E-value=2.3e+02 Score=24.16 Aligned_cols=6 Identities=0% Similarity=-0.169 Sum_probs=2.5
Q ss_pred cCCCCC
Q 041877 55 LGNKLE 60 (254)
Q Consensus 55 ~~~yp~ 60 (254)
+|-|.+
T Consensus 102 RN~YIs 107 (192)
T PF05529_consen 102 RNMYIS 107 (192)
T ss_pred HhHHHH
Confidence 344443
No 204
>PF14662 CCDC155: Coiled-coil region of CCDC155
Probab=20.34 E-value=3.5e+02 Score=23.94 Aligned_cols=38 Identities=32% Similarity=0.428 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Q 041877 85 RRARWKTKQLEKDYEVLKKQFEALKADNDSLQAQNKKL 122 (254)
Q Consensus 85 RRak~Kr~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l 122 (254)
|+.-...++.+++...+-.++++|..+|..+..+.+.+
T Consensus 84 ~~L~aq~rqlEkE~q~L~~~i~~Lqeen~kl~~e~~~l 121 (193)
T PF14662_consen 84 RSLLAQARQLEKEQQSLVAEIETLQEENGKLLAERDGL 121 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhhhhH
Confidence 33333334444444444444444444444444443333
No 205
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=20.23 E-value=4.2e+02 Score=28.05 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=14.4
Q ss_pred CCHHHHHHHHHHhCCChhhhh
Q 041877 59 LEPERKLQLARALGLQPRQIA 79 (254)
Q Consensus 59 p~~~~r~~LA~~LgL~~rqV~ 79 (254)
|....=.++|+.+||++..|.
T Consensus 480 ~g~S~a~~iA~~~Glp~~ii~ 500 (771)
T TIGR01069 480 PGESYAFEIAQRYGIPHFIIE 500 (771)
T ss_pred CCCcHHHHHHHHhCcCHHHHH
Confidence 344455678888888887665
No 206
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=20.20 E-value=1.4e+02 Score=29.85 Aligned_cols=13 Identities=31% Similarity=0.312 Sum_probs=9.3
Q ss_pred CCCHHHHHHHHHH
Q 041877 40 RLNLEQVKALEKS 52 (254)
Q Consensus 40 r~t~~Ql~~LE~~ 52 (254)
++|.+....|.+.
T Consensus 220 ~LteeEkrLL~kE 232 (472)
T KOG0709|consen 220 VLTEEEKRLLTKE 232 (472)
T ss_pred eccHHHHHHHHhc
Confidence 5788877777665
No 207
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=20.12 E-value=3.8e+02 Score=21.67 Aligned_cols=44 Identities=27% Similarity=0.324 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhccCCC
Q 041877 92 KQLEKDYEVLKKQFEALKADNDSLQAQNKKLHAELVSLKNKDSN 135 (254)
Q Consensus 92 ~~~~~~~~~lk~~~~~l~~e~~~l~~e~~~l~~e~~~lk~~~~~ 135 (254)
...+...-.+-+++..++..-..+-.||-.|+-|+..|+.+...
T Consensus 11 ~~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~ 54 (114)
T COG4467 11 DNLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence 45666777888999999999999999999999999999988654
Done!