Query psy9565
Match_columns 288
No_of_seqs 298 out of 1715
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 22:52:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9565.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9565hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0486|consensus 99.9 1.1E-21 2.5E-26 174.9 8.1 67 89-160 109-175 (351)
2 KOG0488|consensus 99.8 1.7E-21 3.7E-26 178.8 8.6 76 85-160 165-240 (309)
3 KOG0484|consensus 99.8 2.3E-22 5E-27 152.1 2.1 65 85-149 10-74 (125)
4 KOG0485|consensus 99.8 6.6E-20 1.4E-24 156.0 11.4 65 87-151 99-163 (268)
5 KOG0842|consensus 99.8 5.3E-20 1.2E-24 166.7 7.3 64 88-151 149-212 (307)
6 KOG0489|consensus 99.8 3.7E-20 8E-25 167.1 5.6 61 90-150 157-217 (261)
7 KOG2251|consensus 99.8 1E-19 2.2E-24 155.7 6.4 64 87-150 32-95 (228)
8 KOG0843|consensus 99.8 8.4E-20 1.8E-24 151.4 4.3 65 89-153 99-163 (197)
9 KOG0487|consensus 99.8 2E-19 4.3E-24 163.1 7.0 67 85-151 228-294 (308)
10 KOG0494|consensus 99.8 2.5E-19 5.4E-24 156.0 6.9 66 91-161 140-205 (332)
11 KOG0850|consensus 99.8 1.3E-18 2.7E-23 149.7 8.0 63 88-150 118-180 (245)
12 KOG0492|consensus 99.7 1.5E-18 3.2E-23 146.9 4.2 69 90-158 142-210 (246)
13 KOG0848|consensus 99.7 4.4E-18 9.4E-23 149.0 4.7 66 90-155 197-262 (317)
14 KOG0849|consensus 99.7 5.9E-17 1.3E-21 151.9 9.6 133 15-148 97-232 (354)
15 KOG0844|consensus 99.7 1.4E-17 3.1E-22 148.1 3.9 62 88-149 177-238 (408)
16 TIGR01565 homeo_ZF_HD homeobox 99.7 1.1E-16 2.3E-21 111.1 5.4 52 93-144 2-57 (58)
17 KOG0491|consensus 99.7 4.4E-17 9.5E-22 133.3 3.3 60 91-150 99-158 (194)
18 PF00046 Homeobox: Homeobox do 99.6 1E-16 2.2E-21 111.5 4.2 55 93-147 1-55 (57)
19 KOG0493|consensus 99.6 1.2E-16 2.5E-21 139.6 4.9 59 93-151 247-305 (342)
20 smart00389 HOX Homeodomain. DN 99.5 7.5E-15 1.6E-19 101.4 5.1 55 93-147 1-55 (56)
21 KOG0483|consensus 99.5 1.2E-14 2.7E-19 124.9 3.9 55 96-150 54-108 (198)
22 cd00086 homeodomain Homeodomai 99.5 2.8E-14 6.2E-19 99.4 4.7 54 94-147 2-55 (59)
23 COG5576 Homeodomain-containing 99.5 2.2E-14 4.8E-19 119.3 4.6 61 92-152 51-111 (156)
24 KOG3802|consensus 99.5 6.6E-14 1.4E-18 129.7 8.1 60 91-150 293-352 (398)
25 KOG4577|consensus 99.4 4.2E-14 9.1E-19 125.2 3.1 60 92-151 167-226 (383)
26 KOG0847|consensus 99.4 8.1E-14 1.7E-18 119.1 3.5 59 90-148 165-223 (288)
27 KOG0490|consensus 99.4 1.2E-13 2.5E-18 122.2 4.6 64 89-157 57-120 (235)
28 PF03826 OAR: OAR domain; Int 99.3 1.6E-12 3.5E-17 70.4 1.1 20 258-277 2-21 (21)
29 KOG1168|consensus 99.0 2E-10 4.3E-15 102.1 1.9 60 90-149 307-366 (385)
30 KOG3862|consensus 98.7 4.1E-09 8.9E-14 93.1 0.5 103 18-121 109-248 (327)
31 KOG0775|consensus 98.6 1.2E-07 2.6E-12 84.1 8.0 50 99-148 183-232 (304)
32 KOG0774|consensus 98.4 6.6E-07 1.4E-11 78.9 6.7 59 92-150 188-249 (334)
33 KOG0490|consensus 98.3 5.3E-07 1.2E-11 79.5 4.0 64 85-148 146-209 (235)
34 KOG2252|consensus 98.3 5.9E-07 1.3E-11 86.8 4.3 57 91-147 419-475 (558)
35 PF05920 Homeobox_KN: Homeobox 98.2 7.1E-07 1.5E-11 57.4 1.3 33 113-145 7-39 (40)
36 KOG1146|consensus 97.7 7.2E-05 1.6E-09 78.9 6.4 60 90-149 901-960 (1406)
37 PF00292 PAX: 'Paired box' dom 97.4 1.3E-05 2.9E-10 64.1 -2.3 25 18-42 101-125 (125)
38 KOG3517|consensus 97.3 0.00013 2.8E-09 64.3 2.1 30 17-46 103-132 (334)
39 PF11569 Homez: Homeodomain le 96.7 0.0013 2.8E-08 45.1 2.3 42 104-145 10-51 (56)
40 KOG0773|consensus 95.4 0.037 8E-07 52.0 6.5 56 92-147 239-297 (342)
41 KOG3623|consensus 94.7 0.027 5.9E-07 56.8 3.5 48 99-147 564-611 (1007)
42 PF04218 CENP-B_N: CENP-B N-te 94.5 0.052 1.1E-06 36.9 3.5 46 93-143 1-46 (53)
43 KOG1924|consensus 91.2 1.4 3E-05 45.4 9.4 7 106-112 478-484 (1102)
44 PF04967 HTH_10: HTH DNA bindi 81.2 2.8 6E-05 28.5 3.7 41 99-139 1-43 (53)
45 PF04545 Sigma70_r4: Sigma-70, 76.6 3.4 7.5E-05 27.1 3.1 41 98-143 4-44 (50)
46 cd06171 Sigma70_r4 Sigma70, re 73.8 3.6 7.8E-05 26.2 2.7 44 98-146 10-53 (55)
47 cd00569 HTH_Hin_like Helix-tur 70.9 10 0.00023 21.4 4.1 38 98-140 5-42 (42)
48 PF01527 HTH_Tnp_1: Transposas 69.0 2.9 6.4E-05 29.7 1.5 43 94-140 2-44 (76)
49 smart00351 PAX Paired Box doma 68.9 1.8 3.8E-05 34.7 0.3 24 19-42 102-125 (125)
50 KOG1146|consensus 67.5 4.8 0.0001 43.9 3.2 56 92-147 444-499 (1406)
51 TIGR03879 near_KaiC_dom probab 66.9 2.2 4.9E-05 31.0 0.5 35 108-142 21-55 (73)
52 PF08281 Sigma70_r4_2: Sigma-7 63.8 10 0.00022 25.0 3.2 41 99-144 11-51 (54)
53 PF10668 Phage_terminase: Phag 63.6 3.7 8.1E-05 28.6 1.0 25 121-147 24-48 (60)
54 cd00131 PAX Paired Box domain 60.6 1.7 3.7E-05 34.9 -1.3 25 20-44 103-127 (128)
55 PRK03975 tfx putative transcri 59.9 13 0.00027 30.6 3.7 46 96-147 4-49 (141)
56 COG3413 Predicted DNA binding 58.2 12 0.00027 32.5 3.7 42 98-139 155-198 (215)
57 PF13936 HTH_38: Helix-turn-he 57.2 8.6 0.00019 24.7 1.9 39 97-140 3-41 (44)
58 PF00196 GerE: Bacterial regul 57.2 11 0.00025 25.4 2.6 44 98-147 3-46 (58)
59 PF08280 HTH_Mga: M protein tr 56.4 11 0.00025 25.7 2.5 37 102-142 6-42 (59)
60 PRK10072 putative transcriptio 53.6 7.3 0.00016 29.8 1.2 40 99-145 33-72 (96)
61 cd04761 HTH_MerR-SF Helix-Turn 50.4 8.4 0.00018 24.6 1.0 22 122-143 3-24 (49)
62 PF06056 Terminase_5: Putative 49.7 5.7 0.00012 27.4 0.1 27 119-147 13-39 (58)
63 smart00421 HTH_LUXR helix_turn 49.6 22 0.00048 22.8 3.1 44 98-147 3-46 (58)
64 PRK04217 hypothetical protein; 48.9 22 0.00047 27.9 3.3 46 97-147 41-86 (110)
65 PF09607 BrkDBD: Brinker DNA-b 48.7 31 0.00067 23.9 3.6 44 96-141 3-47 (58)
66 PRK10403 transcriptional regul 47.6 17 0.00036 30.0 2.7 46 97-148 152-197 (215)
67 PF13551 HTH_29: Winged helix- 44.6 45 0.00097 25.0 4.5 48 94-141 53-109 (112)
68 PF08279 HTH_11: HTH domain; 44.4 27 0.00059 23.0 2.9 34 104-140 3-36 (55)
69 COG2944 Predicted transcriptio 44.3 24 0.00051 27.5 2.8 41 98-145 43-83 (104)
70 COG4367 Uncharacterized protei 43.3 33 0.00071 25.9 3.2 39 99-137 3-41 (97)
71 PRK10360 DNA-binding transcrip 43.0 22 0.00047 29.2 2.7 44 98-147 137-180 (196)
72 PRK06424 transcription factor; 41.3 30 0.00066 28.5 3.2 27 120-146 98-124 (144)
73 cd06170 LuxR_C_like C-terminal 40.0 31 0.00067 22.2 2.6 37 100-142 2-38 (57)
74 PF13443 HTH_26: Cro/C1-type H 40.0 16 0.00034 24.8 1.1 27 121-147 12-38 (63)
75 PF13384 HTH_23: Homeodomain-l 38.7 16 0.00036 23.5 1.0 23 119-141 17-39 (50)
76 PF13411 MerR_1: MerR HTH fami 38.6 17 0.00036 25.2 1.1 20 122-141 3-22 (69)
77 PF13518 HTH_28: Helix-turn-he 38.3 16 0.00036 23.5 1.0 23 121-143 14-36 (52)
78 PRK09413 IS2 repressor TnpA; R 37.7 59 0.0013 25.5 4.3 40 96-140 10-50 (121)
79 PF02796 HTH_7: Helix-turn-hel 36.9 44 0.00095 21.4 2.8 38 98-140 5-42 (45)
80 PF00376 MerR: MerR family reg 36.5 18 0.00039 22.6 0.9 17 123-139 3-19 (38)
81 PRK09935 transcriptional regul 36.0 32 0.00069 28.3 2.6 45 97-147 148-192 (210)
82 cd04762 HTH_MerR-trunc Helix-T 36.0 21 0.00045 22.2 1.2 24 122-145 3-26 (49)
83 PRK00118 putative DNA-binding 33.8 37 0.0008 26.4 2.4 45 98-147 17-61 (104)
84 PRK09646 RNA polymerase sigma 33.5 42 0.00091 28.3 3.0 45 98-147 142-186 (194)
85 PRK06759 RNA polymerase factor 33.4 42 0.00091 26.8 2.9 45 98-147 106-150 (154)
86 cd01392 HTH_LacI Helix-turn-he 33.2 19 0.0004 23.4 0.6 21 124-144 2-22 (52)
87 PRK12514 RNA polymerase sigma 32.7 34 0.00074 28.3 2.3 44 99-147 130-173 (179)
88 PF01381 HTH_3: Helix-turn-hel 32.5 25 0.00055 22.9 1.2 24 121-144 11-34 (55)
89 cd04763 HTH_MlrA-like Helix-Tu 32.3 22 0.00047 24.7 0.8 21 122-142 3-23 (68)
90 PRK12512 RNA polymerase sigma 31.7 50 0.0011 27.4 3.1 45 98-147 131-175 (184)
91 TIGR00721 tfx DNA-binding prot 31.2 62 0.0013 26.4 3.4 46 96-147 4-49 (137)
92 PRK15369 two component system 30.9 51 0.0011 26.7 3.1 44 98-147 149-192 (211)
93 cd04764 HTH_MlrA-like_sg1 Heli 30.5 24 0.00052 24.4 0.8 21 122-142 3-23 (67)
94 KOG3755|consensus 30.4 11 0.00024 37.9 -1.2 60 92-156 691-758 (769)
95 PRK09652 RNA polymerase sigma 30.3 45 0.00098 27.2 2.6 45 98-147 128-172 (182)
96 TIGR02985 Sig70_bacteroi1 RNA 30.3 42 0.00092 26.7 2.4 44 99-147 114-157 (161)
97 PRK12526 RNA polymerase sigma 30.2 61 0.0013 27.7 3.5 45 98-147 153-197 (206)
98 PRK12519 RNA polymerase sigma 29.1 39 0.00085 28.3 2.1 44 99-147 142-185 (194)
99 TIGR02937 sigma70-ECF RNA poly 28.8 48 0.001 25.7 2.4 45 98-147 110-154 (158)
100 PRK09648 RNA polymerase sigma 28.5 57 0.0012 27.2 3.0 46 97-147 138-183 (189)
101 TIGR03070 couple_hipB transcri 28.1 37 0.00079 22.1 1.4 24 121-144 17-40 (58)
102 PF05263 DUF722: Protein of un 27.9 62 0.0014 26.2 2.9 42 98-142 81-122 (130)
103 PRK10651 transcriptional regul 27.8 54 0.0012 27.0 2.7 44 98-147 155-198 (216)
104 PF08880 QLQ: QLQ; InterPro: 27.4 55 0.0012 20.4 1.9 14 98-111 2-15 (37)
105 PF00325 Crp: Bacterial regula 26.4 46 0.001 20.1 1.4 17 121-137 4-20 (32)
106 PF13565 HTH_32: Homeodomain-l 26.3 2.3E+02 0.0049 19.7 5.5 39 100-138 32-75 (77)
107 TIGR03541 reg_near_HchA LuxR f 26.3 58 0.0013 28.6 2.7 47 96-148 169-215 (232)
108 PRK06811 RNA polymerase factor 25.3 84 0.0018 26.3 3.4 45 98-147 131-175 (189)
109 PRK10100 DNA-binding transcrip 25.3 57 0.0012 28.4 2.4 44 98-147 155-198 (216)
110 PRK09480 slmA division inhibit 24.8 69 0.0015 26.4 2.8 38 106-144 18-55 (194)
111 PRK11924 RNA polymerase sigma 24.7 56 0.0012 26.5 2.2 44 99-147 126-169 (179)
112 PF13730 HTH_36: Helix-turn-he 24.6 65 0.0014 21.1 2.1 42 99-141 3-47 (55)
113 TIGR02948 SigW_bacill RNA poly 24.5 65 0.0014 26.6 2.6 45 98-147 136-180 (187)
114 PRK10430 DNA-binding transcrip 24.5 77 0.0017 27.4 3.1 45 98-143 158-202 (239)
115 PRK09639 RNA polymerase sigma 24.3 91 0.002 25.1 3.4 44 98-147 112-155 (166)
116 cd01104 HTH_MlrA-CarA Helix-Tu 24.0 36 0.00078 23.3 0.8 20 122-141 3-22 (68)
117 TIGR02989 Sig-70_gvs1 RNA poly 23.9 67 0.0015 25.7 2.5 45 98-147 111-155 (159)
118 TIGR02999 Sig-70_X6 RNA polyme 23.8 88 0.0019 25.8 3.3 44 99-147 135-178 (183)
119 PRK09642 RNA polymerase sigma 23.6 93 0.002 25.0 3.3 45 98-147 106-150 (160)
120 TIGR02607 antidote_HigA addict 23.5 46 0.00099 23.5 1.2 24 121-144 20-43 (78)
121 TIGR03020 EpsA transcriptional 23.4 87 0.0019 28.1 3.3 47 96-148 188-234 (247)
122 TIGR01764 excise DNA binding d 23.2 45 0.00098 20.7 1.1 23 122-144 4-26 (49)
123 KOG3623|consensus 22.6 68 0.0015 33.4 2.6 54 94-147 628-681 (1007)
124 PRK05602 RNA polymerase sigma 22.6 66 0.0014 26.8 2.2 45 98-147 128-172 (186)
125 PRK05657 RNA polymerase sigma 22.5 85 0.0018 29.3 3.1 50 97-147 261-310 (325)
126 PRK06986 fliA flagellar biosyn 22.2 76 0.0016 27.7 2.6 45 98-147 184-228 (236)
127 smart00027 EH Eps15 homology d 22.2 1.4E+02 0.0031 22.0 3.8 44 98-141 3-51 (96)
128 PF01726 LexA_DNA_bind: LexA D 22.2 1.2E+02 0.0025 21.3 3.1 40 98-139 3-46 (65)
129 PHA01976 helix-turn-helix prot 22.2 51 0.0011 22.5 1.2 24 121-144 17-40 (67)
130 PF13412 HTH_24: Winged helix- 22.1 1.3E+02 0.0028 19.0 3.2 37 100-140 2-38 (48)
131 PF12728 HTH_17: Helix-turn-he 22.0 50 0.0011 21.4 1.1 24 122-145 4-27 (51)
132 PF12824 MRP-L20: Mitochondria 21.7 1.2E+02 0.0027 25.4 3.7 47 95-143 82-128 (164)
133 cd08315 Death_TRAILR_DR4_DR5 D 21.5 93 0.002 23.6 2.6 35 104-138 3-38 (96)
134 cd00093 HTH_XRE Helix-turn-hel 21.5 57 0.0012 20.0 1.3 24 121-144 14-37 (58)
135 PRK09958 DNA-binding transcrip 21.5 92 0.002 25.5 2.9 45 97-147 142-186 (204)
136 TIGR02959 SigZ RNA polymerase 21.2 1.1E+02 0.0024 25.1 3.3 45 98-147 100-144 (170)
137 PRK12515 RNA polymerase sigma 21.0 1.1E+02 0.0023 25.5 3.3 46 97-147 130-175 (189)
138 PRK12543 RNA polymerase sigma 21.0 61 0.0013 26.9 1.7 47 98-149 117-163 (179)
139 TIGR02983 SigE-fam_strep RNA p 21.0 85 0.0018 25.3 2.6 44 99-147 111-154 (162)
140 PRK08301 sporulation sigma fac 20.8 1E+02 0.0022 26.9 3.1 49 98-147 178-226 (234)
141 COG5484 Uncharacterized conser 20.5 43 0.00094 30.2 0.7 33 114-148 14-46 (279)
142 PF12802 MarR_2: MarR family; 20.5 1.5E+02 0.0032 19.6 3.3 37 99-137 3-39 (62)
143 PF13404 HTH_AsnC-type: AsnC-t 20.4 60 0.0013 20.6 1.2 18 120-137 18-35 (42)
144 PRK06288 RNA polymerase sigma 20.3 74 0.0016 28.5 2.2 45 98-147 212-256 (268)
145 PRK09644 RNA polymerase sigma 20.3 81 0.0018 25.6 2.3 45 98-147 108-152 (165)
146 PRK12541 RNA polymerase sigma 20.3 79 0.0017 25.5 2.2 45 98-147 112-156 (161)
147 PF07638 Sigma70_ECF: ECF sigm 20.2 83 0.0018 26.5 2.4 30 118-147 150-179 (185)
148 PRK08583 RNA polymerase sigma 20.1 89 0.0019 27.7 2.7 45 98-147 205-249 (257)
149 PRK11511 DNA-binding transcrip 20.0 83 0.0018 24.8 2.2 31 113-143 19-49 (127)
No 1
>KOG0486|consensus
Probab=99.85 E-value=1.1e-21 Score=174.94 Aligned_cols=67 Identities=37% Similarity=0.470 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchhhhhhhccCC
Q psy9565 89 SNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVSTVTINNTLNP 160 (288)
Q Consensus 89 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~~~~~~~~~~ 160 (288)
..|+||.||.||.+||.+||..|+++.|||+..|+|||..++|+|.+|+|||.|||+|| |++|+...
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakw-----rkrErN~~ 175 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKW-----RKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhh-----hhhhhhHH
Confidence 34788999999999999999999999999999999999999999999999999999999 65555544
No 2
>KOG0488|consensus
Probab=99.85 E-value=1.7e-21 Score=178.85 Aligned_cols=76 Identities=32% Similarity=0.379 Sum_probs=66.9
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchhhhhhhccCC
Q psy9565 85 SCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVSTVTINNTLNP 160 (288)
Q Consensus 85 ~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~~~~~~~~~~ 160 (288)
....++|+|+.||.||..||.+||+.|++++|.++.+|.+||..|||+..|||+||||||+||||++....+....
T Consensus 165 ~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~~~ 240 (309)
T KOG0488|consen 165 QRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELLYQ 240 (309)
T ss_pred ccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhccccc
Confidence 3345588889999999999999999999999999999999999999999999999999999998876664443333
No 3
>KOG0484|consensus
Probab=99.85 E-value=2.3e-22 Score=152.11 Aligned_cols=65 Identities=48% Similarity=0.672 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccc
Q psy9565 85 SCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDV 149 (288)
Q Consensus 85 ~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~ 149 (288)
+...++|+||-||+||..||.+||+.|...+|||++.|+|||.++.|+|.+|||||||||+|.++
T Consensus 10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK 74 (125)
T KOG0484|consen 10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK 74 (125)
T ss_pred ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence 44567888999999999999999999999999999999999999999999999999999999943
No 4
>KOG0485|consensus
Probab=99.82 E-value=6.6e-20 Score=155.95 Aligned_cols=65 Identities=23% Similarity=0.295 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchh
Q psy9565 87 KSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVST 151 (288)
Q Consensus 87 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~ 151 (288)
....++||.||+|+..|+..||..|+..+|++..+|..||.+|.|+|+||||||||||.||||+-
T Consensus 99 ~g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 99 LGDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 34456788999999999999999999999999999999999999999999999999999996553
No 5
>KOG0842|consensus
Probab=99.80 E-value=5.3e-20 Score=166.68 Aligned_cols=64 Identities=30% Similarity=0.372 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchh
Q psy9565 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVST 151 (288)
Q Consensus 88 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~ 151 (288)
..+++||.|-.||+.|..+||+.|..++|++..+||+||..|+||++||||||||||.|.||+.
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 3567778899999999999999999999999999999999999999999999999999997753
No 6
>KOG0489|consensus
Probab=99.80 E-value=3.7e-20 Score=167.09 Aligned_cols=61 Identities=31% Similarity=0.361 Sum_probs=57.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccch
Q psy9565 90 NKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVS 150 (288)
Q Consensus 90 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~ 150 (288)
.+.||.||.||..||.+||++|+.++|+++..|.|||..|.|+|+||||||||||+||||.
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999999999999999999999999999999999999999999544
No 7
>KOG2251|consensus
Probab=99.79 E-value=1e-19 Score=155.72 Aligned_cols=64 Identities=47% Similarity=0.649 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccch
Q psy9565 87 KSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVS 150 (288)
Q Consensus 87 ~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~ 150 (288)
..++|.||.||+||.+||++||.+|.+.+|||+..|++||.+|+|.+.+|||||+|||+|+|++
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 5678899999999999999999999999999999999999999999999999999999999554
No 8
>KOG0843|consensus
Probab=99.78 E-value=8.4e-20 Score=151.41 Aligned_cols=65 Identities=34% Similarity=0.366 Sum_probs=60.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchhhh
Q psy9565 89 SNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVSTVT 153 (288)
Q Consensus 89 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~~~ 153 (288)
..+.||.||.||.+||..||..|+.++|....+|++||+.|+|++.||||||||||+|.||+..+
T Consensus 99 ~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 99 SMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred ccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 34788999999999999999999999999999999999999999999999999999999776444
No 9
>KOG0487|consensus
Probab=99.78 E-value=2e-19 Score=163.05 Aligned_cols=67 Identities=28% Similarity=0.280 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchh
Q psy9565 85 SCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVST 151 (288)
Q Consensus 85 ~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~ 151 (288)
+....+..||||..||+.|+.+||++|-.|.|.+...|.||++.|+|||+||||||||||+|.||..
T Consensus 228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 3445577788999999999999999999999999999999999999999999999999999997764
No 10
>KOG0494|consensus
Probab=99.78 E-value=2.5e-19 Score=156.05 Aligned_cols=66 Identities=38% Similarity=0.478 Sum_probs=59.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchhhhhhhccCCC
Q psy9565 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVSTVTINNTLNPA 161 (288)
Q Consensus 91 k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~~~~~~~~~~~ 161 (288)
|+|+.||.||..|+++||+.|+..+|||++.|+.||.++.|.|.+|||||||||+|| ||.++.+..
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKW-----Rk~Ek~wg~ 205 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKW-----RKTEKRWGG 205 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHh-----hhhhhhcCc
Confidence 334449999999999999999999999999999999999999999999999999999 666655544
No 11
>KOG0850|consensus
Probab=99.76 E-value=1.3e-18 Score=149.71 Aligned_cols=63 Identities=30% Similarity=0.377 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccch
Q psy9565 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVS 150 (288)
Q Consensus 88 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~ 150 (288)
..+|.|+.||.|+..||..|.+.|++++|+-..+|.|||..|||+.+||||||||||.|.||+
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 456778889999999999999999999999999999999999999999999999999999544
No 12
>KOG0492|consensus
Probab=99.73 E-value=1.5e-18 Score=146.89 Aligned_cols=69 Identities=32% Similarity=0.340 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchhhhhhhcc
Q psy9565 90 NKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVSTVTINNTL 158 (288)
Q Consensus 90 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~~~~~~~~ 158 (288)
+..|+.||.||.+||..||+.|...+|+++.+|.|++..|.|+++||||||||||+|.||.+.-..++.
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~ 210 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKL 210 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHh
Confidence 345778999999999999999999999999999999999999999999999999999977644444443
No 13
>KOG0848|consensus
Probab=99.71 E-value=4.4e-18 Score=148.98 Aligned_cols=66 Identities=26% Similarity=0.254 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchhhhhh
Q psy9565 90 NKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVSTVTIN 155 (288)
Q Consensus 90 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~~~~~ 155 (288)
|.+.|.|-+||..|..+||++|...+|.++..+.|||..|+|+||||||||||||+|.+|..+|+.
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 344567899999999999999999999999999999999999999999999999999988877774
No 14
>KOG0849|consensus
Probab=99.69 E-value=5.9e-17 Score=151.94 Aligned_cols=133 Identities=23% Similarity=0.220 Sum_probs=92.3
Q ss_pred CccccccccCCCCCCCCCCCCCccccccCCCCCCCccCCCCCCCCCCCCCCCCCCCCC---ccCCCCCCCCCCCCCCCCC
Q psy9565 15 NSDLKVNNENECDDSNRLPSSESSRHLYFTDSNSDLKVNNENECDDSNRLPSSESSRH---HISRHLSLSPISSCKSSNK 91 (288)
Q Consensus 15 ~~~~rll~E~vCd~d~vpSvSSinriir~~~s~~~~~~~~~~~~~~s~~~~~s~s~~~---~~~~~~s~~~~~~~~~~~k 91 (288)
....+|+.|++|+.++.|+|++|+|+++......+-.......... .....+..... .......+.........++
T Consensus 97 ~ir~~l~~~~~~~~~t~Ps~ssi~r~~r~~~~~~d~~~~~~~~~~~-~~~~~~~~~gs~~~~s~~~~~~~~~p~~~~~~~ 175 (354)
T KOG0849|consen 97 EIRDQLLHEGLCTQATLPSVSSINRVLRNGALGKDQGLPSQQVTKE-KSPSISGALGSQAGASLLSADDEEPPGYALQRG 175 (354)
T ss_pred hhhhcccCcccccCCCCCChhhhhHHhhcccccccccccccccccc-ccCCcccccCCccccccccCCcccccccccccc
Confidence 3456789999999999999999999999665433220000000000 00000000000 0000111122334556677
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhcccc
Q psy9565 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLID 148 (288)
Q Consensus 92 ~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k 148 (288)
.+|.||.|+..|++.||+.|++++||++..|++||.+++|++.+|+|||+|||++|+
T Consensus 176 ~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~r 232 (354)
T KOG0849|consen 176 GRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWR 232 (354)
T ss_pred ccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhh
Confidence 888899999999999999999999999999999999999999999999999999993
No 15
>KOG0844|consensus
Probab=99.68 E-value=1.4e-17 Score=148.07 Aligned_cols=62 Identities=31% Similarity=0.369 Sum_probs=58.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccc
Q psy9565 88 SSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDV 149 (288)
Q Consensus 88 ~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~ 149 (288)
....-||.||.||.+|+..||++|-+..|.++..|.|||..|||.|+.|||||||||+|+||
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKR 238 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKR 238 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhh
Confidence 44556899999999999999999999999999999999999999999999999999999943
No 16
>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=99.66 E-value=1.1e-16 Score=111.06 Aligned_cols=52 Identities=17% Similarity=0.294 Sum_probs=50.4
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCC----CCHHhHHHHHHhcCCChhhhcccccchh
Q psy9565 93 RRSRTNFTLEQLNELERLFDETHY----PDAFMREELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 93 rr~Rt~ft~~Ql~~Le~~F~~~~y----p~~~~r~~La~~l~l~~~~v~vWFqnrR 144 (288)
||.||.||.+|++.||..|+..+| |+..+|++||..|||++++|||||||.+
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 789999999999999999999999 9999999999999999999999999964
No 17
>KOG0491|consensus
Probab=99.66 E-value=4.4e-17 Score=133.28 Aligned_cols=60 Identities=32% Similarity=0.456 Sum_probs=56.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccch
Q psy9565 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVS 150 (288)
Q Consensus 91 k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~ 150 (288)
++++.||+|+..||..||+.|+.++|.+..+|.|||..|+|+++|||.||||||+|.||.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~ 158 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQ 158 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999999999999999999999999999999999999999999544
No 18
>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=99.65 E-value=1e-16 Score=111.46 Aligned_cols=55 Identities=45% Similarity=0.611 Sum_probs=53.7
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 93 RRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 93 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
||+|+.||.+|+..||..|..++||+..++++||..|||+..+|++||+|+|.++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 55 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKE 55 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHh
Confidence 5789999999999999999999999999999999999999999999999999998
No 19
>KOG0493|consensus
Probab=99.64 E-value=1.2e-16 Score=139.57 Aligned_cols=59 Identities=41% Similarity=0.540 Sum_probs=55.8
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchh
Q psy9565 93 RRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVST 151 (288)
Q Consensus 93 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~ 151 (288)
||.||.||.+||..|+.+|+.++|.....|.+||.+|+|.|.||||||||+|+|.||.+
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 56799999999999999999999999999999999999999999999999999996543
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.54 E-value=7.5e-15 Score=101.42 Aligned_cols=55 Identities=47% Similarity=0.623 Sum_probs=52.3
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 93 RRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 93 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
++.|+.|+.+|+..||..|..++||+..++.+||..+||+..+|++||+|+|.+.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 3567889999999999999999999999999999999999999999999999886
No 21
>KOG0483|consensus
Probab=99.50 E-value=1.2e-14 Score=124.88 Aligned_cols=55 Identities=22% Similarity=0.274 Sum_probs=52.0
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccch
Q psy9565 96 RTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVS 150 (288)
Q Consensus 96 Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~ 150 (288)
...||.+|...||+.|+...|.....+..||..|||.++||.|||||||++||.+
T Consensus 54 k~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 54 KRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred cccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 3469999999999999999999999999999999999999999999999999864
No 22
>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=99.49 E-value=2.8e-14 Score=99.37 Aligned_cols=54 Identities=44% Similarity=0.630 Sum_probs=52.3
Q ss_pred CCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 94 RSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 94 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
+.|+.|+.+|+..||..|..++||+..++.+||..+||++.+|++||+|+|.+.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKL 55 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 567899999999999999999999999999999999999999999999999998
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.49 E-value=2.2e-14 Score=119.32 Aligned_cols=61 Identities=30% Similarity=0.273 Sum_probs=55.1
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchhh
Q psy9565 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVSTV 152 (288)
Q Consensus 92 ~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~~ 152 (288)
.+++|+..|.+|+.+|++.|+.++||+...|.+|+..|||+++-|||||||||++.|+...
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred CcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 4556666799999999999999999999999999999999999999999999999965533
No 24
>KOG3802|consensus
Probab=99.48 E-value=6.6e-14 Score=129.70 Aligned_cols=60 Identities=17% Similarity=0.175 Sum_probs=57.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccch
Q psy9565 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVS 150 (288)
Q Consensus 91 k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~ 150 (288)
|+||+||.|+......||++|.+|+.|+..+..+||.+|+|...+|+|||+|||.|.||.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 778899999999999999999999999999999999999999999999999999999654
No 25
>KOG4577|consensus
Probab=99.44 E-value=4.2e-14 Score=125.23 Aligned_cols=60 Identities=28% Similarity=0.347 Sum_probs=57.4
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchh
Q psy9565 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVST 151 (288)
Q Consensus 92 ~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~ 151 (288)
.||.||++|..||+.|+..|+-.+.|.+..||+|+..+||.-++|||||||||+|.||.+
T Consensus 167 nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 167 NKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred cCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 478999999999999999999999999999999999999999999999999999998763
No 26
>KOG0847|consensus
Probab=99.42 E-value=8.1e-14 Score=119.11 Aligned_cols=59 Identities=31% Similarity=0.439 Sum_probs=55.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhcccc
Q psy9565 90 NKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLID 148 (288)
Q Consensus 90 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k 148 (288)
.+++-.|-+|+-+|+..||+.|+..+|+-..+|.+||..||+++.||+|||||||+||+
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWR 223 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWR 223 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhh
Confidence 44556788999999999999999999999999999999999999999999999999993
No 27
>KOG0490|consensus
Probab=99.42 E-value=1.2e-13 Score=122.20 Aligned_cols=64 Identities=34% Similarity=0.346 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccchhhhhhhc
Q psy9565 89 SNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVSTVTINNT 157 (288)
Q Consensus 89 ~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~~~~~~~~ 157 (288)
..++||.||.|+.+|+++||+.|+..+|||...|++||..++|++.+|||||||||+|| +++++
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~-----r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKD-----RKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhh-----hhhhc
Confidence 55678999999999999999999999999999999999999999999999999999999 65554
No 28
>PF03826 OAR: OAR domain; InterPro: IPR003654 This 14 amino acid motif has been identified within the C-terminal region of several Paired-like homeodomain (HD) containing proteins [, ]. It was named OAR domain after the initials of otp, aristaless, and rax []. Although it has been proposed that this domain could be important for transactivation and be involved in protein-protein interactions or DNA binding [, ], is function is not yet known. Some proteins known to contain a OAR domain include human RIEG, defects in which are the cause of Rieger syndrome []; human OG12X and Mus musculus (Mouse) Og12x, whose function is not yet known []; vertebrate Rax, which plays a role in the proliferation and/or differentiation of retinal cells []; Drosophila DRX, which appears to be important in brain development []; and human SHOX, encoded by the short stature homeobox-containing gene. Defects or lack of this protein are the cause of short stature associated with the Turner syndrome [].; GO: 0003677 DNA binding, 0007275 multicellular organismal development, 0005634 nucleus
Probab=99.25 E-value=1.6e-12 Score=70.37 Aligned_cols=20 Identities=60% Similarity=0.702 Sum_probs=18.4
Q ss_pred CCCchhHHHHHHhhHHHHHH
Q psy9565 258 LSKNSSIADLRLKAKKHAEA 277 (288)
Q Consensus 258 ~~r~SSIAaLRlKAkeH~~~ 277 (288)
|+|+||||+||||||||+++
T Consensus 2 d~r~sSIa~LRlKAkeH~~~ 21 (21)
T PF03826_consen 2 DRRSSSIAALRLKAKEHSAA 21 (21)
T ss_pred CcchhhHHHHHHHHHHhccC
Confidence 78999999999999999863
No 29
>KOG1168|consensus
Probab=98.96 E-value=2e-10 Score=102.15 Aligned_cols=60 Identities=17% Similarity=0.193 Sum_probs=56.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccc
Q psy9565 90 NKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDV 149 (288)
Q Consensus 90 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~ 149 (288)
..+||+||.+..-....||.+|..++.|+......+|++|.|...+|+|||+|+|.|.||
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 346789999999999999999999999999999999999999999999999999999944
No 30
>KOG3862|consensus
Probab=98.68 E-value=4.1e-09 Score=93.13 Aligned_cols=103 Identities=18% Similarity=0.318 Sum_probs=61.6
Q ss_pred ccccccCCCCCCCCCCCCCccccccCCCCCCCccC---------CC-CCCCCCCCCCCCCCCCCCccCCCCCCCCCCCCC
Q psy9565 18 LKVNNENECDDSNRLPSSESSRHLYFTDSNSDLKV---------NN-ENECDDSNRLPSSESSRHHISRHLSLSPISSCK 87 (288)
Q Consensus 18 ~rll~E~vCd~d~vpSvSSinriir~~~s~~~~~~---------~~-~~~~~~s~~~~~s~s~~~~~~~~~s~~~~~~~~ 87 (288)
=||++|++||+|+|++|++||||||++......-. .. +.........+.+....++.. .+++++..+..
T Consensus 109 ~~l~~~~ic~~d~vpsVssinri~r~~~~~~~~~~~~s~vsk~l~~~h~a~~s~~~~P~~~~~~~s~~-~~Si~~~~~~a 187 (327)
T KOG3862|consen 109 DRLLAEPICDNDTVPSVSSINRIIRTKVQQKQLGITHSCVTKVLARGHTAVPSSASPPPSSVQSDSVG-SYSINGLLGIA 187 (327)
T ss_pred hhhhcccccCCCCCchHHHHHHHHHHhhhhcccCCccchhhccccCcccccccCCCCCCCCcccCCCC-ceeeccccccc
Confidence 47999999999999999999999997654222111 11 112222222333333333333 44433322221
Q ss_pred CCC--------------------------CCCC-CCCCCCHHHHHHHHHHhhhCCCCCHHh
Q psy9565 88 SSN--------------------------KQRR-SRTNFTLEQLNELERLFDETHYPDAFM 121 (288)
Q Consensus 88 ~~~--------------------------k~rr-~Rt~ft~~Ql~~Le~~F~~~~yp~~~~ 121 (288)
.+. .++. .-..||..+++.|+..|++.+|++++.
T Consensus 188 ~pss~~~~~~~~~~~~s~~~~~~~~~~~~prk~l~~d~ft~~~~~~ld~~~~r~~y~~~~~ 248 (327)
T KOG3862|consen 188 QPSSAKRKMDDSDQEGSVPSIDSQSGSSGPRKHLRADAFTQQHLEPLDRSFERPHYPLVYA 248 (327)
T ss_pred cCccccccCCcccccCcccccCCCccccCcchhcccccccccccccccceeeccccccccc
Confidence 110 1111 125799999999999999999998764
No 31
>KOG0775|consensus
Probab=98.62 E-value=1.2e-07 Score=84.11 Aligned_cols=50 Identities=20% Similarity=0.266 Sum_probs=45.2
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhcccc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLID 148 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k 148 (288)
|...-...|...|..++||+..++.|||+++||+.+||-+||+|||.++|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 44444568999999999999999999999999999999999999999993
No 32
>KOG0774|consensus
Probab=98.40 E-value=6.6e-07 Score=78.94 Aligned_cols=59 Identities=24% Similarity=0.383 Sum_probs=54.5
Q ss_pred CCCCCCCCCHHHHHHHHHHhhh---CCCCCHHhHHHHHHhcCCChhhhcccccchhccccch
Q psy9565 92 QRRSRTNFTLEQLNELERLFDE---THYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDVS 150 (288)
Q Consensus 92 ~rr~Rt~ft~~Ql~~Le~~F~~---~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~~ 150 (288)
.||+|..|+..-.++|..+|.. ++||+...+++||.+.|++-.||-.||.|+|-+.||.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 4778889999999999999974 7999999999999999999999999999999999654
No 33
>KOG0490|consensus
Probab=98.30 E-value=5.3e-07 Score=79.55 Aligned_cols=64 Identities=41% Similarity=0.467 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhcccc
Q psy9565 85 SCKSSNKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLID 148 (288)
Q Consensus 85 ~~~~~~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k 148 (288)
......+.++.|+.|...|+..|+..|...+||+...++.|+..+|+++..|+|||||+|.+++
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~ 209 (235)
T KOG0490|consen 146 KGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLR 209 (235)
T ss_pred cCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHH
Confidence 3445566788999999999999999999999999999999999999999999999999999993
No 34
>KOG2252|consensus
Probab=98.29 E-value=5.9e-07 Score=86.81 Aligned_cols=57 Identities=30% Similarity=0.343 Sum_probs=53.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 91 KQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 91 k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
+.||.|.+||..|...|...|+.++||+..+.+.|+.+|||....|.+||-|-|.+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 457789999999999999999999999999999999999999999999999987764
No 35
>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=98.17 E-value=7.1e-07 Score=57.36 Aligned_cols=33 Identities=27% Similarity=0.416 Sum_probs=28.1
Q ss_pred hCCCCCHHhHHHHHHhcCCChhhhcccccchhc
Q psy9565 113 ETHYPDAFMREELSQRLGLSEARVQNFSQVLNL 145 (288)
Q Consensus 113 ~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~ 145 (288)
.++||+..++++||..+||+..||..||-|.|.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 479999999999999999999999999999875
No 36
>KOG1146|consensus
Probab=97.67 E-value=7.2e-05 Score=78.90 Aligned_cols=60 Identities=20% Similarity=0.164 Sum_probs=56.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccc
Q psy9565 90 NKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDV 149 (288)
Q Consensus 90 ~k~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~ 149 (288)
-.+|++||.|+.+||..|...|..+.||...+.|.|...++|..++|+|||||-|.|.|+
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k 960 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKK 960 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhh
Confidence 345788999999999999999999999999999999999999999999999999999944
No 37
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=97.41 E-value=1.3e-05 Score=64.14 Aligned_cols=25 Identities=28% Similarity=0.292 Sum_probs=20.3
Q ss_pred ccccccCCCCCCCCCCCCCcccccc
Q psy9565 18 LKVNNENECDDSNRLPSSESSRHLY 42 (288)
Q Consensus 18 ~rll~E~vCd~d~vpSvSSinriir 42 (288)
-+|++|++|+.+++|||||||||+|
T Consensus 101 ~~L~~~gvc~~~~~PsvssInRilr 125 (125)
T PF00292_consen 101 DRLIADGVCDRSNVPSVSSINRILR 125 (125)
T ss_dssp HHHHHTTSS-TTTS--HHHHHHHHH
T ss_pred HHHHHcCCCCCCCCCCHHHHHHhhC
Confidence 4799999999999999999999986
No 38
>KOG3517|consensus
Probab=97.29 E-value=0.00013 Score=64.31 Aligned_cols=30 Identities=23% Similarity=0.150 Sum_probs=26.9
Q ss_pred cccccccCCCCCCCCCCCCCccccccCCCC
Q psy9565 17 DLKVNNENECDDSNRLPSSESSRHLYFTDS 46 (288)
Q Consensus 17 ~~rll~E~vCd~d~vpSvSSinriir~~~s 46 (288)
.-|||+|||||.-+|||||||+||+|++..
T Consensus 103 RDRLlsdgiCDk~NvPSVSSISRILRNKiG 132 (334)
T KOG3517|consen 103 RDRLLSDGICDKYNVPSVSSISRILRNKIG 132 (334)
T ss_pred hhhhhhcccccccCCcchHHHHHHHHhhhc
Confidence 348999999999999999999999997743
No 39
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.67 E-value=0.0013 Score=45.08 Aligned_cols=42 Identities=14% Similarity=0.121 Sum_probs=31.2
Q ss_pred HHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhc
Q psy9565 104 LNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNL 145 (288)
Q Consensus 104 l~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~ 145 (288)
+..|+++|...+++....-.+|..+.+|+..||+.||-.|+.
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 345999999999999999999999999999999999976643
No 40
>KOG0773|consensus
Probab=95.43 E-value=0.037 Score=51.95 Aligned_cols=56 Identities=21% Similarity=0.318 Sum_probs=46.7
Q ss_pred CCCCCCCCCHHHHHHHHHH-hh--hCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 92 QRRSRTNFTLEQLNELERL-FD--ETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 92 ~rr~Rt~ft~~Ql~~Le~~-F~--~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
..|.+..|......+|+.. |+ ..+||+..++..||.++||+..||.+||-|.|-+.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~ 297 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRL 297 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhccccc
Confidence 3445567888888888876 33 24799999999999999999999999999988766
No 41
>KOG3623|consensus
Probab=94.74 E-value=0.027 Score=56.80 Aligned_cols=48 Identities=17% Similarity=0.155 Sum_probs=44.0
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
|+.- +..|..+|..+..|+..+-..+|.+.||+.+.|++||++++++.
T Consensus 564 ~~~p-~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e 611 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEE 611 (1007)
T ss_pred cCCc-HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhh
Confidence 4444 78899999999999999999999999999999999999999887
No 42
>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=94.49 E-value=0.052 Score=36.88 Aligned_cols=46 Identities=22% Similarity=0.421 Sum_probs=35.1
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccch
Q psy9565 93 RRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVL 143 (288)
Q Consensus 93 rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnr 143 (288)
||+|..+|-+|-..+=..++... ...+||..+|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 57888999999887777787766 57899999999999999999885
No 43
>KOG1924|consensus
Probab=91.22 E-value=1.4 Score=45.37 Aligned_cols=7 Identities=71% Similarity=1.118 Sum_probs=3.1
Q ss_pred HHHHHhh
Q psy9565 106 ELERLFD 112 (288)
Q Consensus 106 ~Le~~F~ 112 (288)
+|++.|+
T Consensus 478 e~~kk~~ 484 (1102)
T KOG1924|consen 478 ELEKKFD 484 (1102)
T ss_pred HHHHHHH
Confidence 4444443
No 44
>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=81.23 E-value=2.8 Score=28.50 Aligned_cols=41 Identities=27% Similarity=0.367 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHhhhCC--CCCHHhHHHHHHhcCCChhhhccc
Q psy9565 99 FTLEQLNELERLFDETH--YPDAFMREELSQRLGLSEARVQNF 139 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~--yp~~~~r~~La~~l~l~~~~v~vW 139 (288)
+|..|.+.|...|+..= +|-...-.+||..||++...|..-
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence 58899999999998764 466777899999999999876543
No 45
>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=76.64 E-value=3.4 Score=27.05 Aligned_cols=41 Identities=17% Similarity=0.316 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccch
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVL 143 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnr 143 (288)
.+++.|..+|...| -....-.++|..+|++...|+.+...-
T Consensus 4 ~L~~~er~vi~~~y-----~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRY-----FEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHH-----TST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-----cCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 46888999999988 233456889999999999999876443
No 46
>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=73.84 E-value=3.6 Score=26.24 Aligned_cols=44 Identities=16% Similarity=0.169 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhcc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLL 146 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k 146 (288)
.++..+...++..|. ....-.++|..+|++..+|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~-----~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFG-----EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 467778777777663 23456788999999999999998665443
No 47
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=70.89 E-value=10 Score=21.43 Aligned_cols=38 Identities=29% Similarity=0.457 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFS 140 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWF 140 (288)
.++..+...+...|... + ...++|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 36677776666666532 2 56788999999999988774
No 48
>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=69.04 E-value=2.9 Score=29.70 Aligned_cols=43 Identities=19% Similarity=0.254 Sum_probs=27.6
Q ss_pred CCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccc
Q psy9565 94 RSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFS 140 (288)
Q Consensus 94 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWF 140 (288)
++|..||.++...+=..+. .......++|..+|+++.++..|-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHH
Confidence 4567899998776655441 223567889999999999999994
No 49
>smart00351 PAX Paired Box domain.
Probab=68.89 E-value=1.8 Score=34.68 Aligned_cols=24 Identities=29% Similarity=0.374 Sum_probs=20.9
Q ss_pred cccccCCCCCCCCCCCCCcccccc
Q psy9565 19 KVNNENECDDSNRLPSSESSRHLY 42 (288)
Q Consensus 19 rll~E~vCd~d~vpSvSSinriir 42 (288)
.|.++|||....+|++|.|+++++
T Consensus 102 ~L~~~gv~~~~~~Ps~sti~~~l~ 125 (125)
T smart00351 102 RLLSEGVCDKDNVPSVSSINRILR 125 (125)
T ss_pred HHHHcCCCcCCCCCChhhHHHhhC
Confidence 455689999999999999999875
No 50
>KOG1146|consensus
Probab=67.49 E-value=4.8 Score=43.88 Aligned_cols=56 Identities=18% Similarity=0.062 Sum_probs=51.1
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 92 QRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 92 ~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+-.|+.++.-|+.+|...|....||.-.++..++..|++..+.+-.||++++.+|
T Consensus 444 ~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~ 499 (1406)
T KOG1146|consen 444 PLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKA 499 (1406)
T ss_pred hhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHh
Confidence 34467889999999999999999999999999999999999999999999988888
No 51
>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=66.90 E-value=2.2 Score=30.96 Aligned_cols=35 Identities=20% Similarity=0.171 Sum_probs=29.1
Q ss_pred HHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccc
Q psy9565 108 ERLFDETHYPDAFMREELSQRLGLSEARVQNFSQV 142 (288)
Q Consensus 108 e~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqn 142 (288)
+..|....|-......++|..||+++..|+.|+.+
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 44577667667778899999999999999999865
No 52
>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=63.83 E-value=10 Score=25.03 Aligned_cols=41 Identities=17% Similarity=0.162 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchh
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR 144 (288)
++..+..++...| .....-.++|..+|+++..|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4555656665544 3455678999999999999999986533
No 53
>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=63.64 E-value=3.7 Score=28.63 Aligned_cols=25 Identities=16% Similarity=0.363 Sum_probs=19.7
Q ss_pred hHHHHHHhcCCChhhhcccccchhccc
Q psy9565 121 MREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 121 ~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.-.+||.+||+++.+|+.|= .+-+|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK--~~dkW 48 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK--SRDKW 48 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh--hhcch
Confidence 45679999999999999993 34455
No 54
>cd00131 PAX Paired Box domain
Probab=60.57 E-value=1.7 Score=34.95 Aligned_cols=25 Identities=32% Similarity=0.303 Sum_probs=21.3
Q ss_pred ccccCCCCCCCCCCCCCccccccCC
Q psy9565 20 VNNENECDDSNRLPSSESSRHLYFT 44 (288)
Q Consensus 20 ll~E~vCd~d~vpSvSSinriir~~ 44 (288)
|..+|+|.++..+|+|.|+|+++.+
T Consensus 103 L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 103 LLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred HHHcCCcccCCCCCHHHHHHHHHhc
Confidence 4567999999999999999998753
No 55
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=59.85 E-value=13 Score=30.63 Aligned_cols=46 Identities=22% Similarity=0.215 Sum_probs=37.7
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 96 RTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 96 Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
...+|+.|..+|+..+ ......++|..||++...|+.|.++.+.|.
T Consensus 4 ~~~Lt~rqreVL~lr~------~GlTq~EIAe~LGiS~~tVs~ie~ra~kkL 49 (141)
T PRK03975 4 ESFLTERQIEVLRLRE------RGLTQQEIADILGTSRANVSSIEKRARENI 49 (141)
T ss_pred ccCCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3578999999997732 335578999999999999999998877777
No 56
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=58.25 E-value=12 Score=32.50 Aligned_cols=42 Identities=24% Similarity=0.438 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHhhhC--CCCCHHhHHHHHHhcCCChhhhccc
Q psy9565 98 NFTLEQLNELERLFDET--HYPDAFMREELSQRLGLSEARVQNF 139 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~--~yp~~~~r~~La~~l~l~~~~v~vW 139 (288)
.+|..|+++|...|... -||-...-.+||++||++...+.--
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~eh 198 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEH 198 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHH
Confidence 69999999999999876 4577778899999999999876543
No 57
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=57.22 E-value=8.6 Score=24.72 Aligned_cols=39 Identities=28% Similarity=0.433 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccc
Q psy9565 97 TNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFS 140 (288)
Q Consensus 97 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWF 140 (288)
..||.+|...++..++. .....++|..||.+...|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~-----G~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ-----GMSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHc-----CCCHHHHHHHHCcCcHHHHHHH
Confidence 46888899999887653 3456789999999999988765
No 58
>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=57.21 E-value=11 Score=25.35 Aligned_cols=44 Identities=23% Similarity=0.358 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.||..++++|+.... .....++|..+|+++..|..+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~------G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ------GMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHT------TS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh------cCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 578899998877664 34478999999999999999988776665
No 59
>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=56.38 E-value=11 Score=25.72 Aligned_cols=37 Identities=30% Similarity=0.412 Sum_probs=27.1
Q ss_pred HHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccc
Q psy9565 102 EQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQV 142 (288)
Q Consensus 102 ~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqn 142 (288)
-|+..|+-.|. +...+. .+||..||++++.|+....+
T Consensus 6 rq~~Ll~~L~~-~~~~~~---~ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITL---KELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHHH-HTSBBH---HHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcH---HHHHHHHCCCHHHHHHHHHH
Confidence 47788888888 554444 49999999999999876543
No 60
>PRK10072 putative transcriptional regulator; Provisional
Probab=53.55 E-value=7.3 Score=29.80 Aligned_cols=40 Identities=15% Similarity=0.243 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNL 145 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~ 145 (288)
.+...+..|...-. ....+||..+|++...|..|.+.+|.
T Consensus 33 ~~~~eik~LR~~~g-------lTQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTG-------LKIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcC-------CCHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 36666666644322 23789999999999999999988764
No 61
>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=50.40 E-value=8.4 Score=24.63 Aligned_cols=22 Identities=18% Similarity=0.333 Sum_probs=18.5
Q ss_pred HHHHHHhcCCChhhhcccccch
Q psy9565 122 REELSQRLGLSEARVQNFSQVL 143 (288)
Q Consensus 122 r~~La~~l~l~~~~v~vWFqnr 143 (288)
..++|+.+|++...|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4688999999999999996543
No 62
>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=49.71 E-value=5.7 Score=27.42 Aligned_cols=27 Identities=15% Similarity=0.297 Sum_probs=22.4
Q ss_pred HHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 119 AFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 119 ~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
...-.++|..||++..+|..|- .|.+|
T Consensus 13 G~~~~eIA~~Lg~~~~TV~~W~--~r~~W 39 (58)
T PF06056_consen 13 GWSIKEIAEELGVPRSTVYSWK--DRYKW 39 (58)
T ss_pred CCCHHHHHHHHCCChHHHHHHH--HhhCc
Confidence 4556889999999999999995 46666
No 63
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=49.65 E-value=22 Score=22.83 Aligned_cols=44 Identities=23% Similarity=0.341 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..+...++..+. .....++|..+|++...|..|.+.-+.|.
T Consensus 3 ~l~~~e~~i~~~~~~------g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRLLAE------GLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 467888887765432 23568899999999999999876544443
No 64
>PRK04217 hypothetical protein; Provisional
Probab=48.92 E-value=22 Score=27.93 Aligned_cols=46 Identities=22% Similarity=0.198 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 97 TNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 97 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
..++.+|.+++...|...- ...++|+.+|++...|+..+..-+.+.
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3578999888877664332 678899999999999999887766666
No 65
>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=48.72 E-value=31 Score=23.90 Aligned_cols=44 Identities=18% Similarity=0.317 Sum_probs=22.5
Q ss_pred CCCCCHHH-HHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhccccc
Q psy9565 96 RTNFTLEQ-LNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQ 141 (288)
Q Consensus 96 Rt~ft~~Q-l~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFq 141 (288)
|..|+..- |.++|. |..+..--...|. -|.++|+++.+|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~-a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEY-AEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHH-HHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHH-HHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 34455543 445554 4333333333444 49999999999999954
No 66
>PRK10403 transcriptional regulator NarP; Provisional
Probab=47.56 E-value=17 Score=30.02 Aligned_cols=46 Identities=20% Similarity=0.250 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhcccc
Q psy9565 97 TNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLID 148 (288)
Q Consensus 97 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k 148 (288)
..+|..+.++|+...+. ..+.++|..++++++.|+++..|=+.|..
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 35899999988765432 55789999999999999999988877763
No 67
>PF13551 HTH_29: Winged helix-turn helix
Probab=44.55 E-value=45 Score=25.01 Aligned_cols=48 Identities=23% Similarity=0.338 Sum_probs=31.0
Q ss_pred CCCCCCCHHHHHHHHHHhhhCCCCC--HHhHHHHHHh-------cCCChhhhccccc
Q psy9565 94 RSRTNFTLEQLNELERLFDETHYPD--AFMREELSQR-------LGLSEARVQNFSQ 141 (288)
Q Consensus 94 r~Rt~ft~~Ql~~Le~~F~~~~yp~--~~~r~~La~~-------l~l~~~~v~vWFq 141 (288)
+.+..++.++...|...+..++.-. ......|+.. +.++...|.-|++
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3444489999999999998765321 2333444443 3677788887764
No 68
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=44.38 E-value=27 Score=22.97 Aligned_cols=34 Identities=21% Similarity=0.294 Sum_probs=22.1
Q ss_pred HHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccc
Q psy9565 104 LNELERLFDETHYPDAFMREELSQRLGLSEARVQNFS 140 (288)
Q Consensus 104 l~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWF 140 (288)
...|+..++...+ ..-.+||..|+++.+.|+--.
T Consensus 3 ~~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 3 KQILKLLLESKEP---ITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHHHH
Confidence 3445444444443 567899999999999887543
No 69
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=44.30 E-value=24 Score=27.48 Aligned_cols=41 Identities=12% Similarity=0.246 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNL 145 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~ 145 (288)
.++..++..+.+.+... +.+.|..||++...|+.|=|+|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 38888999888877644 477899999999999999888753
No 70
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.31 E-value=33 Score=25.86 Aligned_cols=39 Identities=15% Similarity=0.219 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~ 137 (288)
++++|...-...|+.+--.+....+++|..||.++..|+
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 567787777777777766777788999999999986554
No 71
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=42.98 E-value=22 Score=29.20 Aligned_cols=44 Identities=23% Similarity=0.229 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+|..+.+.|+..++- ..+.++|..++++++.|++..++=|.|.
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 5888888888776542 3788999999999999999988877765
No 72
>PRK06424 transcription factor; Provisional
Probab=41.33 E-value=30 Score=28.46 Aligned_cols=27 Identities=7% Similarity=0.044 Sum_probs=22.7
Q ss_pred HhHHHHHHhcCCChhhhcccccchhcc
Q psy9565 120 FMREELSQRLGLSEARVQNFSQVLNLL 146 (288)
Q Consensus 120 ~~r~~La~~l~l~~~~v~vWFqnrR~k 146 (288)
...++||..+|++...|.-|..+++.-
T Consensus 98 LSQ~eLA~~iGvs~stIskiE~G~~~P 124 (144)
T PRK06424 98 MSQADLAAKIFERKNVIASIERGDLLP 124 (144)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCCCCC
Confidence 346789999999999999999887653
No 73
>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=40.02 E-value=31 Score=22.23 Aligned_cols=37 Identities=24% Similarity=0.280 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccc
Q psy9565 100 TLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQV 142 (288)
Q Consensus 100 t~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqn 142 (288)
+..|...+...+. .....++|+.++++...|+.|...
T Consensus 2 ~~~e~~i~~~~~~------~~s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 2 TPREREVLRLLAE------GKTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4556666655332 236788999999999999999753
No 74
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=40.02 E-value=16 Score=24.83 Aligned_cols=27 Identities=11% Similarity=0.170 Sum_probs=18.6
Q ss_pred hHHHHHHhcCCChhhhcccccchhccc
Q psy9565 121 MREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 121 ~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
...+||+.+|++..+|.-|+.++...+
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 567899999999999999999875444
No 75
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=38.68 E-value=16 Score=23.54 Aligned_cols=23 Identities=26% Similarity=0.517 Sum_probs=17.8
Q ss_pred HHhHHHHHHhcCCChhhhccccc
Q psy9565 119 AFMREELSQRLGLSEARVQNFSQ 141 (288)
Q Consensus 119 ~~~r~~La~~l~l~~~~v~vWFq 141 (288)
.....++|..||++..+|..|.+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 45678899999999999999964
No 76
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=38.59 E-value=17 Score=25.15 Aligned_cols=20 Identities=20% Similarity=0.473 Sum_probs=17.3
Q ss_pred HHHHHHhcCCChhhhccccc
Q psy9565 122 REELSQRLGLSEARVQNFSQ 141 (288)
Q Consensus 122 r~~La~~l~l~~~~v~vWFq 141 (288)
..++|+.+|++..+|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45899999999999999943
No 77
>PF13518 HTH_28: Helix-turn-helix domain
Probab=38.27 E-value=16 Score=23.54 Aligned_cols=23 Identities=17% Similarity=0.358 Sum_probs=19.4
Q ss_pred hHHHHHHhcCCChhhhcccccch
Q psy9565 121 MREELSQRLGLSEARVQNFSQVL 143 (288)
Q Consensus 121 ~r~~La~~l~l~~~~v~vWFqnr 143 (288)
...++|.++|++..+|..|.+.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHH
Confidence 46679999999999999997543
No 78
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=37.68 E-value=59 Score=25.52 Aligned_cols=40 Identities=10% Similarity=0.201 Sum_probs=27.2
Q ss_pred CCCCCHHHHH-HHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccc
Q psy9565 96 RTNFTLEQLN-ELERLFDETHYPDAFMREELSQRLGLSEARVQNFS 140 (288)
Q Consensus 96 Rt~ft~~Ql~-~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWF 140 (288)
|..||.++.. .+...+. + .....++|..+|+++.+|..|.
T Consensus 10 rr~ys~EfK~~aV~~~~~-~----g~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE-P----GMTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred CCCCCHHHHHHHHHHHHc-C----CCCHHHHHHHHCcCHHHHHHHH
Confidence 3457777644 4444343 2 2345788999999999999994
No 79
>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=36.93 E-value=44 Score=21.36 Aligned_cols=38 Identities=24% Similarity=0.516 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFS 140 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWF 140 (288)
.++.+|.+.+-..+... ....++|..+|++...|.-|+
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 46776777777777655 347889999999999887654
No 80
>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=36.53 E-value=18 Score=22.57 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=14.7
Q ss_pred HHHHHhcCCChhhhccc
Q psy9565 123 EELSQRLGLSEARVQNF 139 (288)
Q Consensus 123 ~~La~~l~l~~~~v~vW 139 (288)
-++|+.+|++...|+.|
T Consensus 3 ~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHCCCHHHHHHH
Confidence 47899999999999999
No 81
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=36.04 E-value=32 Score=28.34 Aligned_cols=45 Identities=18% Similarity=0.194 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 97 TNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 97 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
..+|..+...|+..++- ..+.++|..|+++.+.|+++..+=|.|.
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 35788888888654433 6789999999999999999988877776
No 82
>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=35.95 E-value=21 Score=22.24 Aligned_cols=24 Identities=21% Similarity=0.351 Sum_probs=20.2
Q ss_pred HHHHHHhcCCChhhhcccccchhc
Q psy9565 122 REELSQRLGLSEARVQNFSQVLNL 145 (288)
Q Consensus 122 r~~La~~l~l~~~~v~vWFqnrR~ 145 (288)
..++|..||++...|..|.++...
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 468999999999999999876543
No 83
>PRK00118 putative DNA-binding protein; Validated
Probab=33.77 E-value=37 Score=26.36 Aligned_cols=45 Identities=18% Similarity=0.211 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..++...|.. ...-.++|..+|+++..|..|...-|.+.
T Consensus 17 ~L~ekqRevl~L~y~e-----g~S~~EIAe~lGIS~~TV~r~L~RArkkL 61 (104)
T PRK00118 17 LLTEKQRNYMELYYLD-----DYSLGEIAEEFNVSRQAVYDNIKRTEKLL 61 (104)
T ss_pred cCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3566777777555433 34567899999999999999987666665
No 84
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=33.52 E-value=42 Score=28.31 Aligned_cols=45 Identities=13% Similarity=0.114 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..+|...| .....-.++|..||++...|+.+...-|.+.
T Consensus 142 ~L~~~~r~vl~l~~-----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~L 186 (194)
T PRK09646 142 ALTDTQRESVTLAY-----YGGLTYREVAERLAVPLGTVKTRMRDGLIRL 186 (194)
T ss_pred hCCHHHHHHHHHHH-----HcCCCHHHHHHHhCCChHhHHHHHHHHHHHH
Confidence 46677777776544 2335568999999999999999986666665
No 85
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=33.43 E-value=42 Score=26.80 Aligned_cols=45 Identities=7% Similarity=-0.120 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+++.|..++...|- ....-.|+|..+|+++..|+.|...-+.+.
T Consensus 106 ~L~~~~r~ii~l~~~-----~~~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 106 VLDEKEKYIIFERFF-----VGKTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred hCCHHHHHHHHHHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456666666655442 335578999999999999999976555444
No 86
>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=33.18 E-value=19 Score=23.37 Aligned_cols=21 Identities=19% Similarity=0.216 Sum_probs=19.3
Q ss_pred HHHHhcCCChhhhcccccchh
Q psy9565 124 ELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 124 ~La~~l~l~~~~v~vWFqnrR 144 (288)
+||+.+|++...|.-|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 689999999999999999874
No 87
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=32.71 E-value=34 Score=28.28 Aligned_cols=44 Identities=11% Similarity=0.234 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
++..+..++...| .....-+++|..||+++..|+++...-|.+.
T Consensus 130 L~~~~r~i~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 130 LEKDRAAAVRRAY-----LEGLSYKELAERHDVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence 4555555555444 3345578999999999999999987666555
No 88
>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=32.51 E-value=25 Score=22.95 Aligned_cols=24 Identities=21% Similarity=0.441 Sum_probs=19.6
Q ss_pred hHHHHHHhcCCChhhhcccccchh
Q psy9565 121 MREELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 121 ~r~~La~~l~l~~~~v~vWFqnrR 144 (288)
...+||..+|++...|.-|..+++
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHhCCCcchhHHHhcCCC
Confidence 358899999999999999998854
No 89
>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=32.26 E-value=22 Score=24.73 Aligned_cols=21 Identities=10% Similarity=0.173 Sum_probs=18.1
Q ss_pred HHHHHHhcCCChhhhcccccc
Q psy9565 122 REELSQRLGLSEARVQNFSQV 142 (288)
Q Consensus 122 r~~La~~l~l~~~~v~vWFqn 142 (288)
..++|+.+|++...++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 468999999999999999653
No 90
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=31.71 E-value=50 Score=27.42 Aligned_cols=45 Identities=13% Similarity=0.073 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..+..+|...|- ....-.++|..||++...|+.++..-|.+.
T Consensus 131 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~l~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 131 TLPPRQRDVVQSISV-----EGASIKETAAKLSMSEGAVRVALHRGLAAL 175 (184)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 456666666665432 244568999999999999999987766666
No 91
>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=31.17 E-value=62 Score=26.42 Aligned_cols=46 Identities=22% Similarity=0.195 Sum_probs=36.7
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 96 RTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 96 Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+.+|..|..+|+..+ ......++|..||++...|..|-..-+.|.
T Consensus 4 ~~~Lte~qr~VL~Lr~------~GlTq~EIAe~LgiS~stV~~~e~ra~kkL 49 (137)
T TIGR00721 4 KTFLTERQIKVLELRE------KGLSQKEIAKELKTTRANVSAIEKRAMENI 49 (137)
T ss_pred cCCCCHHHHHHHHHHH------cCCCHHHHHHHHCcCHHHHHHHHHhHHHHH
Confidence 4678999999998742 234678999999999999999976666665
No 92
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=30.89 E-value=51 Score=26.71 Aligned_cols=44 Identities=16% Similarity=0.214 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+|..+.++|+. +..+ | ...++|+.+++++..|+.|.+|=+.|.
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKL 192 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 488888888876 4322 2 367899999999999999998876665
No 93
>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=30.46 E-value=24 Score=24.36 Aligned_cols=21 Identities=14% Similarity=0.355 Sum_probs=18.0
Q ss_pred HHHHHHhcCCChhhhcccccc
Q psy9565 122 REELSQRLGLSEARVQNFSQV 142 (288)
Q Consensus 122 r~~La~~l~l~~~~v~vWFqn 142 (288)
-.++|+.+|++..+|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999654
No 94
>KOG3755|consensus
Probab=30.41 E-value=11 Score=37.89 Aligned_cols=60 Identities=15% Similarity=-0.045 Sum_probs=0.0
Q ss_pred CCCCCCCCCHHHHHHHHHH-hhhCCCCCHHhHHHHHHhcCCChhh-------hcccccchhccccchhhhhhh
Q psy9565 92 QRRSRTNFTLEQLNELERL-FDETHYPDAFMREELSQRLGLSEAR-------VQNFSQVLNLLIDVSTVTINN 156 (288)
Q Consensus 92 ~rr~Rt~ft~~Ql~~Le~~-F~~~~yp~~~~r~~La~~l~l~~~~-------v~vWFqnrR~k~k~~~~~~~~ 156 (288)
.|+++..|=..|..++... |-+++.+....-.+--+.+.|.+-. |+.||.|||.+. ++.+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~-----~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEE-----KRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHH-----hhhh
No 95
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=30.27 E-value=45 Score=27.17 Aligned_cols=45 Identities=11% Similarity=0.028 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+++.+..+|...|- ....-.++|..||+++..|+.|...-+.+.
T Consensus 128 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~L 172 (182)
T PRK09652 128 SLPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREAL 172 (182)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 577777777776542 234567899999999999999987555554
No 96
>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=30.25 E-value=42 Score=26.66 Aligned_cols=44 Identities=11% Similarity=-0.019 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
++..+...|...| .......++|..+|+++..|+.+...-+.|.
T Consensus 114 L~~~~r~il~l~~-----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 114 LPEQCRKIFILSR-----FEGKSYKEIAEELGISVKTVEYHISKALKEL 157 (161)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4555555555433 2344578899999999999999876555554
No 97
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=30.23 E-value=61 Score=27.70 Aligned_cols=45 Identities=16% Similarity=0.212 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..+|... |.....-.++|..+|+++..|+++...-+.+.
T Consensus 153 ~L~~~~r~vl~l~-----~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 197 (206)
T PRK12526 153 KLPEAQQTVVKGV-----YFQELSQEQLAQQLNVPLGTVKSRLRLALAKL 197 (206)
T ss_pred hCCHHHHHHHHHH-----HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3555555555543 23445678999999999999999987666655
No 98
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=29.10 E-value=39 Score=28.33 Aligned_cols=44 Identities=20% Similarity=0.269 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
++..+..+|...| .....-.++|..+|++...|+.|+..-|.+.
T Consensus 142 L~~~~~~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 185 (194)
T PRK12519 142 LPESQRQVLELAY-----YEGLSQSEIAKRLGIPLGTVKARARQGLLKL 185 (194)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4555555554433 3445678999999999999999997666665
No 99
>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=28.81 E-value=48 Score=25.65 Aligned_cols=45 Identities=13% Similarity=0.142 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|...+...|- ....-.++|..+|+++..|+.|...-+.|.
T Consensus 110 ~L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 110 KLPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKKL 154 (158)
T ss_pred hCCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456666666655432 234567999999999999999876655554
No 100
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.50 E-value=57 Score=27.22 Aligned_cols=46 Identities=13% Similarity=0.022 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 97 TNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 97 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
..++..|..+++..|-. ...-.|+|..||++...|+.+...-|.+.
T Consensus 138 ~~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 138 DTLPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQHRALARL 183 (189)
T ss_pred HhCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45677777777765433 34578999999999999999875544444
No 101
>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=28.14 E-value=37 Score=22.06 Aligned_cols=24 Identities=8% Similarity=0.140 Sum_probs=21.0
Q ss_pred hHHHHHHhcCCChhhhcccccchh
Q psy9565 121 MREELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 121 ~r~~La~~l~l~~~~v~vWFqnrR 144 (288)
...+||..+|++...|.-|..+++
T Consensus 17 tq~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 17 TQADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 468899999999999999987764
No 102
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=27.93 E-value=62 Score=26.17 Aligned_cols=42 Identities=14% Similarity=0.206 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQV 142 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqn 142 (288)
+++.+...+++-.|... .......+|.++++++++++-|++.
T Consensus 81 ~l~de~k~Ii~lry~~r---~~~TW~~IA~~l~i~erta~r~~~~ 122 (130)
T PF05263_consen 81 TLIDEEKRIIKLRYDRR---SRRTWYQIAQKLHISERTARRWRDR 122 (130)
T ss_pred hhCHHHHHHHHHHHccc---ccchHHHHHHHhCccHHHHHHHHHH
Confidence 45555556665555443 4467889999999999999988653
No 103
>PRK10651 transcriptional regulator NarL; Provisional
Probab=27.75 E-value=54 Score=26.95 Aligned_cols=44 Identities=14% Similarity=0.208 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+|..+.++|+...+- ..-.++|+.|+++++.|+++.+|=|.|.
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 4899999999775532 2467889999999999999999888776
No 104
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=27.41 E-value=55 Score=20.43 Aligned_cols=14 Identities=43% Similarity=0.489 Sum_probs=12.0
Q ss_pred CCCHHHHHHHHHHh
Q psy9565 98 NFTLEQLNELERLF 111 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F 111 (288)
.||..|+.+||.-.
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 69999999998754
No 105
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=26.37 E-value=46 Score=20.09 Aligned_cols=17 Identities=29% Similarity=0.616 Sum_probs=13.0
Q ss_pred hHHHHHHhcCCChhhhc
Q psy9565 121 MREELSQRLGLSEARVQ 137 (288)
Q Consensus 121 ~r~~La~~l~l~~~~v~ 137 (288)
.|.+||..+|++...|-
T Consensus 4 tr~diA~~lG~t~ETVS 20 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVS 20 (32)
T ss_dssp -HHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHhCCcHHHHH
Confidence 57899999999987764
No 106
>PF13565 HTH_32: Homeodomain-like domain
Probab=26.29 E-value=2.3e+02 Score=19.68 Aligned_cols=39 Identities=23% Similarity=0.194 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHhhhCCCCCHHhH-HHHHHhcCC----Chhhhcc
Q psy9565 100 TLEQLNELERLFDETHYPDAFMR-EELSQRLGL----SEARVQN 138 (288)
Q Consensus 100 t~~Ql~~Le~~F~~~~yp~~~~r-~~La~~l~l----~~~~v~v 138 (288)
+.++.+.|.+.+..++..+..+. ..|...+|+ +...|.-
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R 75 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYR 75 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHH
Confidence 78887888888888875555444 446666653 5555543
No 107
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=26.25 E-value=58 Score=28.60 Aligned_cols=47 Identities=15% Similarity=0.108 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhcccc
Q psy9565 96 RTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLID 148 (288)
Q Consensus 96 Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k 148 (288)
...+|..|+++|.-.. ....-.++|..||++++.|+.+..|=+.|.+
T Consensus 169 ~~~Lt~re~evl~~~a------~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 169 AGVLSEREREVLAWTA------LGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred hccCCHHHHHHHHHHH------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 3468888888887643 3356788999999999999999998887774
No 108
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=25.29 E-value=84 Score=26.30 Aligned_cols=45 Identities=16% Similarity=0.115 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+++.|..++...|- ......|+|+.+|++...|+...+.-|.+.
T Consensus 131 ~L~~~~r~i~~l~~~-----~g~s~~EIAe~lgis~~~V~~~l~Ra~~~L 175 (189)
T PRK06811 131 DLEKLDREIFIRRYL-----LGEKIEEIAKKLGLTRSAIDNRLSRGRKKL 175 (189)
T ss_pred hCCHHHHHHHHHHHH-----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 466666666665442 234578999999999999999876655555
No 109
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=25.25 E-value=57 Score=28.42 Aligned_cols=44 Identities=23% Similarity=0.124 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+|+.|+++|+-..+ ...-.++|+.|++++..|+.+..+-..|.
T Consensus 155 ~Lt~rE~~Vl~l~~~------G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 155 LLTHREKEILNKLRI------GASNNEIARSLFISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCHHHHHHHHHHHc------CCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 489999999987665 23467899999999999999998877776
No 110
>PRK09480 slmA division inhibitor protein; Provisional
Probab=24.84 E-value=69 Score=26.44 Aligned_cols=38 Identities=18% Similarity=0.291 Sum_probs=31.8
Q ss_pred HHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchh
Q psy9565 106 ELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 106 ~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR 144 (288)
.....|..+.. +...-.+||.+.|++...+-.+|.|+-
T Consensus 18 aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 18 ALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 34455666667 888999999999999999999999976
No 111
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=24.70 E-value=56 Score=26.52 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
++..+..+|...| .....-.++|..+|+++..|+.|...-|.+.
T Consensus 126 L~~~~r~i~~l~~-----~~~~~~~eIA~~lgis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 126 LPVKQREVFLLRY-----VEGLSYREIAEILGVPVGTVKSRLRRARQLL 169 (179)
T ss_pred CCHHHHHHhhHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4555555554443 2334568999999999999999987666665
No 112
>PF13730 HTH_36: Helix-turn-helix domain
Probab=24.61 E-value=65 Score=21.08 Aligned_cols=42 Identities=19% Similarity=0.053 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHhh---hCCCCCHHhHHHHHHhcCCChhhhccccc
Q psy9565 99 FTLEQLNELERLFD---ETHYPDAFMREELSQRLGLSEARVQNFSQ 141 (288)
Q Consensus 99 ft~~Ql~~Le~~F~---~~~yp~~~~r~~La~~l~l~~~~v~vWFq 141 (288)
++..+..++-..+. .+.+ .-.....||..+|++.+.|+-+..
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 34444444433322 2333 444688999999999999987764
No 113
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.50 E-value=65 Score=26.60 Aligned_cols=45 Identities=11% Similarity=0.025 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+++.+..+++..| .....-.++|..||+++..|+++++.-|.+.
T Consensus 136 ~L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 136 ALPPKYRMVIVLKY-----MEDLSLKEISEILDLPVGTVKTRIHRGREAL 180 (187)
T ss_pred hCCHHHhHHhhhHH-----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45666666665533 2345678999999999999999987666665
No 114
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=24.45 E-value=77 Score=27.44 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccch
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVL 143 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnr 143 (288)
.+|..++++|..... .+|-....-.++|.+|++++.+|+..+.+-
T Consensus 158 ~Lt~re~~~l~~~i~-~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWID-AHQDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHH-hCCCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 478888777765554 335556677899999999999999988754
No 115
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=24.31 E-value=91 Score=25.14 Aligned_cols=44 Identities=18% Similarity=0.207 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..+|...| ....-.++|..+|+++..|+.+...-|.+.
T Consensus 112 ~L~~~~r~il~l~~------~g~s~~eIA~~lgis~~tV~~~i~ra~~~L 155 (166)
T PRK09639 112 KMTERDRTVLLLRF------SGYSYKEIAEALGIKESSVGTTLARAKKKF 155 (166)
T ss_pred cCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45666666665555 334578999999999999999986666665
No 116
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=24.04 E-value=36 Score=23.31 Aligned_cols=20 Identities=10% Similarity=0.262 Sum_probs=17.6
Q ss_pred HHHHHHhcCCChhhhccccc
Q psy9565 122 REELSQRLGLSEARVQNFSQ 141 (288)
Q Consensus 122 r~~La~~l~l~~~~v~vWFq 141 (288)
..++|+.+|++..+|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46899999999999999964
No 117
>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=23.90 E-value=67 Score=25.71 Aligned_cols=45 Identities=16% Similarity=0.152 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..++...| .....-.++|..+|++...|+++...-|.+.
T Consensus 111 ~L~~~~r~v~~l~~-----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 111 KLPERQRELLQLRY-----QRGVSLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred HCCHHHHHHHHHHH-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 46666666666543 3345678999999999999998865544443
No 118
>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=23.81 E-value=88 Score=25.75 Aligned_cols=44 Identities=20% Similarity=0.180 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
++..|..++...|- ....-.++|..||+++..|++....-|.+.
T Consensus 135 Lp~~~r~v~~l~~~-----~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 178 (183)
T TIGR02999 135 VDPRQAEVVELRFF-----AGLTVEEIAELLGVSVRTVERDWRFARAWL 178 (183)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 56666666655432 234568999999999999999987665555
No 119
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=23.61 E-value=93 Score=25.01 Aligned_cols=45 Identities=7% Similarity=-0.063 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..++...|- ....-.|+|..||+++..|++++..-|.+.
T Consensus 106 ~Lp~~~r~v~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 150 (160)
T PRK09642 106 ELPENYRDVVLAHYL-----EEKSYQEIALQEKIEVKTVEMKLYRARKWI 150 (160)
T ss_pred hCCHHHHHHHHHHHH-----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 355566565554432 223457999999999999999987666665
No 120
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=23.49 E-value=46 Score=23.46 Aligned_cols=24 Identities=17% Similarity=0.228 Sum_probs=20.8
Q ss_pred hHHHHHHhcCCChhhhcccccchh
Q psy9565 121 MREELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 121 ~r~~La~~l~l~~~~v~vWFqnrR 144 (288)
...+||+.+|++...|.-|+.+++
T Consensus 20 t~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 20 SIRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 357899999999999999998764
No 121
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=23.43 E-value=87 Score=28.11 Aligned_cols=47 Identities=26% Similarity=0.232 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhcccc
Q psy9565 96 RTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLID 148 (288)
Q Consensus 96 Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k 148 (288)
...+|..+.++|+-.. ......++|..||+++..|+.+.+|=+.|.+
T Consensus 188 ~~~LT~RE~evl~l~a------~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 188 AGLITAREAEILAWVR------DGKTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred ccCCCHHHHHHHHHHH------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 3468999999998654 2345788999999999999999988877763
No 122
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=23.25 E-value=45 Score=20.74 Aligned_cols=23 Identities=26% Similarity=0.267 Sum_probs=19.4
Q ss_pred HHHHHHhcCCChhhhcccccchh
Q psy9565 122 REELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 122 r~~La~~l~l~~~~v~vWFqnrR 144 (288)
..++|+.||++...|.-|.++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 46889999999999999976654
No 123
>KOG3623|consensus
Probab=22.56 E-value=68 Score=33.39 Aligned_cols=54 Identities=13% Similarity=0.126 Sum_probs=37.2
Q ss_pred CCCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 94 RSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 94 r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
+-|+....++...|...++.+--+...+-.-.+..|...+.+|+|||++|+..-
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstp 681 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTP 681 (1007)
T ss_pred cccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCC
Confidence 345666666666677777766555544444445557888899999999998776
No 124
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=22.55 E-value=66 Score=26.76 Aligned_cols=45 Identities=7% Similarity=0.027 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+++.+..+|...| .....-.++|..||++...|+.+...-|.+.
T Consensus 128 ~L~~~~r~i~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 128 ALPERQREAIVLQY-----YQGLSNIEAAAVMDISVDALESLLARGRRAL 172 (186)
T ss_pred hCCHHHHHHhhHHH-----hcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 34555656555543 2334568999999999999999986666665
No 125
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=22.47 E-value=85 Score=29.27 Aligned_cols=50 Identities=20% Similarity=0.195 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 97 TNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 97 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
..++..|..+|+..|... |-......++|..||++..+|+.+...-+.|.
T Consensus 261 ~~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL 310 (325)
T PRK05657 261 FELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRL 310 (325)
T ss_pred HcCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 367888888998877432 23456679999999999999999987666666
No 126
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=22.21 E-value=76 Score=27.75 Aligned_cols=45 Identities=18% Similarity=0.232 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+...|..++...| -....-.++|..+|++...|+.+...-+.+.
T Consensus 184 ~L~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~L 228 (236)
T PRK06986 184 SLPEREQLVLSLYY-----QEELNLKEIGAVLGVSESRVSQIHSQAIKRL 228 (236)
T ss_pred hCCHHHHHHHHhHh-----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34566666665554 3344678999999999999999987776666
No 127
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=22.19 E-value=1.4e+02 Score=21.99 Aligned_cols=44 Identities=11% Similarity=0.167 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHhhh-----CCCCCHHhHHHHHHhcCCChhhhccccc
Q psy9565 98 NFTLEQLNELERLFDE-----THYPDAFMREELSQRLGLSEARVQNFSQ 141 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~-----~~yp~~~~r~~La~~l~l~~~~v~vWFq 141 (288)
.+|.+|+..|...|.. +.+.+..+-.++-..+|+++..|.-+|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3688999999999875 2356666666656667888888877764
No 128
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=22.17 E-value=1.2e+02 Score=21.26 Aligned_cols=40 Identities=33% Similarity=0.468 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHH---hhhCCCCCHHhHHHHHHhcCCC-hhhhccc
Q psy9565 98 NFTLEQLNELERL---FDETHYPDAFMREELSQRLGLS-EARVQNF 139 (288)
Q Consensus 98 ~ft~~Ql~~Le~~---F~~~~yp~~~~r~~La~~l~l~-~~~v~vW 139 (288)
.+|.-|.++|+-. ...+.|| ....|||..+|+. ...|+--
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~--Pt~rEIa~~~g~~S~~tv~~~ 46 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYP--PTVREIAEALGLKSTSTVQRH 46 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCC--CCHHHHHHHhCCCChHHHHHH
Confidence 4678888877654 4557777 4678999999997 6666543
No 129
>PHA01976 helix-turn-helix protein
Probab=22.15 E-value=51 Score=22.49 Aligned_cols=24 Identities=25% Similarity=0.358 Sum_probs=20.4
Q ss_pred hHHHHHHhcCCChhhhcccccchh
Q psy9565 121 MREELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 121 ~r~~La~~l~l~~~~v~vWFqnrR 144 (288)
...+||..+|++...|.-|..+++
T Consensus 17 t~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 17 SAPELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 467899999999999999987654
No 130
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=22.14 E-value=1.3e+02 Score=19.02 Aligned_cols=37 Identities=24% Similarity=0.401 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccc
Q psy9565 100 TLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFS 140 (288)
Q Consensus 100 t~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWF 140 (288)
+..+...|+..++... ..+.+||..+|++...|.--+
T Consensus 2 ~~~~~~Il~~l~~~~~----~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRENPR----ITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHHCTT----S-HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHHcCC----CCHHHHHHHhCCCHHHHHHHH
Confidence 4556777766666222 567899999999998886543
No 131
>PF12728 HTH_17: Helix-turn-helix domain
Probab=22.03 E-value=50 Score=21.35 Aligned_cols=24 Identities=21% Similarity=0.308 Sum_probs=19.8
Q ss_pred HHHHHHhcCCChhhhcccccchhc
Q psy9565 122 REELSQRLGLSEARVQNFSQVLNL 145 (288)
Q Consensus 122 r~~La~~l~l~~~~v~vWFqnrR~ 145 (288)
..|+|+.||++...|.-|.++..-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 468899999999999999865543
No 132
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=21.65 E-value=1.2e+02 Score=25.41 Aligned_cols=47 Identities=21% Similarity=0.353 Sum_probs=37.4
Q ss_pred CCCCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccch
Q psy9565 95 SRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVL 143 (288)
Q Consensus 95 ~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnr 143 (288)
+...+|.+++.++.++-. .-|..+.+..||+++|++..-|.+-.+--
T Consensus 82 k~y~Lt~e~i~Eir~LR~--~DP~~wTr~~LAkkF~~S~~fV~~v~~~~ 128 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRA--EDPEKWTRKKLAKKFNCSPLFVSMVAPAP 128 (164)
T ss_pred ccccCCHHHHHHHHHHHH--cCchHhhHHHHHHHhCCCHHHHHHhcCCC
Confidence 346899999999987654 45678999999999999998887755443
No 133
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.55 E-value=93 Score=23.61 Aligned_cols=35 Identities=29% Similarity=0.296 Sum_probs=24.9
Q ss_pred HHHHHHHhhhC-CCCCHHhHHHHHHhcCCChhhhcc
Q psy9565 104 LNELERLFDET-HYPDAFMREELSQRLGLSEARVQN 138 (288)
Q Consensus 104 l~~Le~~F~~~-~yp~~~~r~~La~~l~l~~~~v~v 138 (288)
.+.|..+|..- .......-.+|+++|||++..|..
T Consensus 3 ~~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~ 38 (96)
T cd08315 3 QETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDV 38 (96)
T ss_pred HhHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHH
Confidence 35677787653 344455667799999999987764
No 134
>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=21.51 E-value=57 Score=20.04 Aligned_cols=24 Identities=25% Similarity=0.472 Sum_probs=20.3
Q ss_pred hHHHHHHhcCCChhhhcccccchh
Q psy9565 121 MREELSQRLGLSEARVQNFSQVLN 144 (288)
Q Consensus 121 ~r~~La~~l~l~~~~v~vWFqnrR 144 (288)
...++|..+|+++..|.-|..+.+
T Consensus 14 s~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 14 TQEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred CHHHHHHHHCCCHHHHHHHHcCCC
Confidence 346899999999999999988764
No 135
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=21.51 E-value=92 Score=25.50 Aligned_cols=45 Identities=9% Similarity=0.276 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 97 TNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 97 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
..+|..+.++|+..+.-. .+.++|..++++++.|++.-.+=|.|.
T Consensus 142 ~~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 142 DSLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred ccCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 358999999998877543 478999999999999999877766665
No 136
>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=21.15 E-value=1.1e+02 Score=25.11 Aligned_cols=45 Identities=16% Similarity=0.147 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..+..+|+..| .....-.++|..||+++..|+.+...-|.+.
T Consensus 100 ~L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 144 (170)
T TIGR02959 100 ELPDEYREAIRLTE-----LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKL 144 (170)
T ss_pred hCCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 46667766666554 2334568999999999999999986666666
No 137
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=21.04 E-value=1.1e+02 Score=25.52 Aligned_cols=46 Identities=11% Similarity=0.151 Sum_probs=34.0
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 97 TNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 97 t~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
..++..|..+|+..|- ....-.++|..+|+++..|++.+..-|.+.
T Consensus 130 ~~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~Rar~~L 175 (189)
T PRK12515 130 AKLSPAHREIIDLVYY-----HEKSVEEVGEIVGIPESTVKTRMFYARKKL 175 (189)
T ss_pred HhCCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3567777777765432 334568899999999999999887767666
No 138
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=21.03 E-value=61 Score=26.85 Aligned_cols=47 Identities=13% Similarity=0.113 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLIDV 149 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k~ 149 (288)
.+++.+..++... |.....-.++|..||+++..|++....-|.+.|+
T Consensus 117 ~Lp~~~r~i~~l~-----~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 117 KLPYKLRQVIILR-----YLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred hCCHHHHHHHHHH-----HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3455555555443 2333456899999999999999998877777744
No 139
>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=21.00 E-value=85 Score=25.26 Aligned_cols=44 Identities=11% Similarity=0.109 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
++..+...|+..| .....-.++|..+|++...|+.+...-|.+.
T Consensus 111 L~~~~r~i~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 111 LPARQRAVVVLRY-----YEDLSEAQVAEALGISVGTVKSRLSRALARL 154 (162)
T ss_pred CCHHHHHHhhhHH-----HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4556666665544 2234568899999999999999876666665
No 140
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.77 E-value=1e+02 Score=26.85 Aligned_cols=49 Identities=12% Similarity=0.191 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..++...|.. .+-....-.++|..||++...|+.+...-|.+.
T Consensus 178 ~Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~L 226 (234)
T PRK08301 178 KLSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIKRL 226 (234)
T ss_pred hCCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4666777777665521 113445578999999999999999876655555
No 141
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=20.52 E-value=43 Score=30.24 Aligned_cols=33 Identities=12% Similarity=0.288 Sum_probs=25.9
Q ss_pred CCCCCHHhHHHHHHhcCCChhhhcccccchhcccc
Q psy9565 114 THYPDAFMREELSQRLGLSEARVQNFSQVLNLLID 148 (288)
Q Consensus 114 ~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~k 148 (288)
+-|.....-.+||++||+++.+|+-|- ||..|+
T Consensus 14 k~yl~gmk~~dIAeklGvspntiksWK--rr~gWs 46 (279)
T COG5484 14 KDYLKGMKLKDIAEKLGVSPNTIKSWK--RRDGWS 46 (279)
T ss_pred HHHHhhccHHHHHHHhCCChHHHHHHH--HhcCCC
Confidence 334444556789999999999999994 678884
No 142
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=20.46 E-value=1.5e+02 Score=19.62 Aligned_cols=37 Identities=30% Similarity=0.399 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhc
Q psy9565 99 FTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQ 137 (288)
Q Consensus 99 ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~ 137 (288)
||..|..+|...+..... .....+||..++++...|.
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs 39 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVS 39 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHH
Confidence 678888888766654432 3467899999999987665
No 143
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=20.37 E-value=60 Score=20.61 Aligned_cols=18 Identities=44% Similarity=0.567 Sum_probs=13.5
Q ss_pred HhHHHHHHhcCCChhhhc
Q psy9565 120 FMREELSQRLGLSEARVQ 137 (288)
Q Consensus 120 ~~r~~La~~l~l~~~~v~ 137 (288)
..-.+||+.+||++..|.
T Consensus 18 ~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVR 35 (42)
T ss_dssp S-HHHHHHHHTS-HHHHH
T ss_pred ccHHHHHHHHCcCHHHHH
Confidence 345789999999998876
No 144
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=20.33 E-value=74 Score=28.52 Aligned_cols=45 Identities=16% Similarity=0.286 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.+++.+..+|...|. ....-.++|..+|++...|+.+...-+.+.
T Consensus 212 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~~~ra~~~L 256 (268)
T PRK06288 212 TLPEREKKVLILYYY-----EDLTLKEIGKVLGVTESRISQLHTKAVLQL 256 (268)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 467777777776653 234568999999999999998876666555
No 145
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=20.29 E-value=81 Score=25.62 Aligned_cols=45 Identities=9% Similarity=-0.057 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..++...| ......+++|..||+++..|++|.+.-|.+.
T Consensus 108 ~L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~tv~~~l~Rar~~L 152 (165)
T PRK09644 108 TLPVIEAQAILLCD-----VHELTYEEAASVLDLKLNTYKSHLFRGRKRL 152 (165)
T ss_pred hCCHHHHHHHHhHH-----HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45555555554332 2334568999999999999999987666666
No 146
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=20.27 E-value=79 Score=25.52 Aligned_cols=45 Identities=24% Similarity=0.081 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..+|.-.| .....-.++|..+|++...|+.+...-|.+.
T Consensus 112 ~L~~~~r~v~~l~~-----~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L 156 (161)
T PRK12541 112 SLPLERRNVLLLRD-----YYGFSYKEIAEMTGLSLAKVKIELHRGRKET 156 (161)
T ss_pred HCCHHHHHHhhhHH-----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45666666665543 2334568999999999999999886655555
No 147
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=20.17 E-value=83 Score=26.49 Aligned_cols=30 Identities=27% Similarity=0.413 Sum_probs=23.8
Q ss_pred CHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 118 DAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 118 ~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
....-+|+|..||++++.|+-.++.=|.+.
T Consensus 150 ~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 150 EGLSVEEIAERLGISERTVRRRLRRARAWL 179 (185)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 445778999999999999998776666444
No 148
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.12 E-value=89 Score=27.71 Aligned_cols=45 Identities=16% Similarity=0.242 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHhHHHHHHhcCCChhhhcccccchhccc
Q psy9565 98 NFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQNFSQVLNLLI 147 (288)
Q Consensus 98 ~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~~v~vWFqnrR~k~ 147 (288)
.++..|..+|...|- ....-.++|..||++...|+.|...-+.+.
T Consensus 205 ~L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tV~~~~~ra~~kL 249 (257)
T PRK08583 205 VLSDREKSIIQCTFI-----ENLSQKETGERLGISQMHVSRLQRQAIKKL 249 (257)
T ss_pred hCCHHHHHHHHHHHh-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 467777777777653 233568999999999999999976555554
No 149
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=20.01 E-value=83 Score=24.80 Aligned_cols=31 Identities=23% Similarity=0.262 Sum_probs=24.9
Q ss_pred hCCCCCHHhHHHHHHhcCCChhhhcccccch
Q psy9565 113 ETHYPDAFMREELSQRLGLSEARVQNFSQVL 143 (288)
Q Consensus 113 ~~~yp~~~~r~~La~~l~l~~~~v~vWFqnr 143 (288)
..++-....-++||..+|++++.++-+|+..
T Consensus 19 ~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 19 EDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445556778999999999999999998765
Done!