Query psy13127
Match_columns 64
No_of_seqs 120 out of 1013
Neff 9.0
Searched_HMMs 46136
Date Fri Aug 16 20:16:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13127.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13127hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0488|consensus 99.6 9.4E-15 2E-19 89.2 5.5 47 18-64 170-216 (309)
2 KOG0842|consensus 99.4 2.1E-13 4.6E-18 83.0 4.4 48 17-64 150-197 (307)
3 TIGR01565 homeo_ZF_HD homeobox 99.4 6.2E-13 1.3E-17 63.8 5.0 44 21-64 2-49 (58)
4 KOG2251|consensus 99.4 5.9E-13 1.3E-17 77.7 4.4 47 18-64 35-81 (228)
5 KOG0484|consensus 99.4 1.1E-13 2.3E-18 73.0 0.9 49 16-64 13-61 (125)
6 KOG0487|consensus 99.4 1.4E-12 3E-17 79.5 5.0 49 16-64 231-279 (308)
7 KOG0843|consensus 99.3 2E-12 4.2E-17 73.7 4.6 46 19-64 101-146 (197)
8 KOG0489|consensus 99.3 8.2E-13 1.8E-17 79.2 2.2 47 18-64 157-203 (261)
9 KOG0850|consensus 99.3 2.3E-12 5E-17 75.7 3.9 47 18-64 120-166 (245)
10 PF00046 Homeobox: Homeobox do 99.3 5.3E-12 1.2E-16 60.0 3.1 44 21-64 1-44 (57)
11 KOG0492|consensus 99.2 3.6E-11 7.8E-16 70.0 4.3 47 18-64 142-188 (246)
12 KOG0485|consensus 99.2 3.1E-11 6.8E-16 70.8 3.8 47 18-64 102-148 (268)
13 smart00389 HOX Homeodomain. DN 99.1 2E-10 4.3E-15 54.1 4.1 43 22-64 2-44 (56)
14 KOG0494|consensus 99.1 3.6E-10 7.7E-15 67.9 5.1 45 20-64 140-185 (332)
15 KOG0493|consensus 99.1 4E-10 8.6E-15 67.7 4.9 44 21-64 247-290 (342)
16 cd00086 homeodomain Homeodomai 99.0 4.4E-10 9.5E-15 53.3 4.1 43 22-64 2-44 (59)
17 KOG0486|consensus 99.0 1.4E-10 3E-15 70.9 2.6 47 18-64 110-156 (351)
18 KOG0848|consensus 99.0 9.1E-11 2E-15 70.5 1.7 47 18-64 197-243 (317)
19 KOG0491|consensus 98.9 1.3E-10 2.8E-15 65.7 -0.7 46 19-64 99-144 (194)
20 KOG0849|consensus 98.8 1.4E-08 3E-13 63.4 4.6 48 17-64 173-220 (354)
21 COG5576 Homeodomain-containing 98.7 7.3E-08 1.6E-12 54.3 5.1 47 18-64 49-95 (156)
22 KOG0490|consensus 98.7 2E-08 4.3E-13 58.6 2.8 48 17-64 57-104 (235)
23 KOG0844|consensus 98.6 1.5E-08 3.3E-13 62.1 1.7 47 18-64 179-225 (408)
24 KOG3802|consensus 98.6 1.5E-07 3.2E-12 59.2 4.7 47 18-64 292-338 (398)
25 KOG0483|consensus 98.2 1.3E-06 2.9E-11 50.9 3.2 44 21-64 51-94 (198)
26 KOG2252|consensus 98.0 9.3E-06 2E-10 53.0 3.7 46 19-64 419-464 (558)
27 KOG0847|consensus 97.9 1.4E-05 3E-10 47.5 2.7 47 18-64 165-211 (288)
28 KOG4577|consensus 97.6 8.2E-05 1.8E-09 45.8 3.5 47 18-64 165-211 (383)
29 KOG0774|consensus 97.2 0.00049 1.1E-08 42.0 3.4 45 20-64 188-235 (334)
30 KOG0775|consensus 97.2 0.0008 1.7E-08 41.2 3.9 38 27-64 183-220 (304)
31 PF05920 Homeobox_KN: Homeobox 97.1 0.00015 3.2E-09 32.3 0.2 24 41-64 7-30 (40)
32 KOG1168|consensus 96.4 0.003 6.6E-08 39.1 2.2 45 19-63 308-352 (385)
33 KOG0490|consensus 96.2 0.0053 1.1E-07 35.8 2.7 46 18-63 151-196 (235)
34 PF04967 HTH_10: HTH DNA bindi 94.3 0.042 9.1E-07 25.8 1.9 36 27-62 1-38 (53)
35 PF04218 CENP-B_N: CENP-B N-te 94.1 0.12 2.7E-06 24.0 3.3 39 21-64 1-39 (53)
36 COG3413 Predicted DNA binding 91.5 0.26 5.7E-06 28.8 2.8 37 26-62 155-193 (215)
37 KOG1146|consensus 86.4 0.87 1.9E-05 33.6 2.9 45 20-64 903-947 (1406)
38 PF11569 Homez: Homeodomain le 83.7 0.54 1.2E-05 22.4 0.7 33 32-64 10-42 (56)
39 PF13936 HTH_38: Helix-turn-he 77.9 1 2.2E-05 20.0 0.5 34 25-63 3-36 (44)
40 PF04545 Sigma70_r4: Sigma-70, 73.2 2.8 6.1E-05 18.7 1.4 33 26-63 4-36 (50)
41 PF15063 TC1: Thyroid cancer p 72.2 4.5 9.7E-05 20.5 2.0 50 6-55 13-62 (79)
42 KOG0773|consensus 68.1 11 0.00023 23.6 3.5 42 23-64 242-286 (342)
43 PF01527 HTH_Tnp_1: Transposas 67.6 6.3 0.00014 18.8 2.0 36 22-62 2-38 (76)
44 PF08880 QLQ: QLQ; InterPro: 67.1 7.5 0.00016 16.8 2.0 16 26-41 2-17 (37)
45 PRK13558 bacterio-opsin activa 66.9 8.8 0.00019 25.8 3.1 38 25-62 606-645 (665)
46 PF08280 HTH_Mga: M protein tr 65.9 4.6 9.9E-05 18.9 1.3 30 30-63 6-35 (59)
47 COG4367 Uncharacterized protei 64.2 13 0.00028 19.4 2.8 35 27-61 3-37 (97)
48 PF02796 HTH_7: Helix-turn-hel 60.6 6.6 0.00014 17.2 1.2 32 26-62 5-36 (45)
49 COG1905 NuoE NADH:ubiquinone o 59.1 20 0.00043 20.6 3.2 36 29-64 25-60 (160)
50 PF12824 MRP-L20: Mitochondria 55.3 38 0.00083 19.4 4.1 37 23-61 82-118 (164)
51 PRK15183 Vi polysaccharide bio 52.9 17 0.00037 19.7 2.2 38 25-62 94-131 (143)
52 PRK03975 tfx putative transcri 52.6 16 0.00035 20.4 2.2 34 24-63 4-37 (141)
53 PF08279 HTH_11: HTH domain; 52.0 12 0.00026 16.7 1.4 13 50-62 18-30 (55)
54 PF10668 Phage_terminase: Phag 51.2 5 0.00011 19.3 -0.0 15 50-64 25-39 (60)
55 PRK05988 formate dehydrogenase 49.7 26 0.00057 19.8 2.7 32 33-64 27-58 (156)
56 TIGR01958 nuoE_fam NADH-quinon 49.6 25 0.00055 19.5 2.7 31 34-64 21-51 (148)
57 PF06971 Put_DNA-bind_N: Putat 49.4 3.9 8.5E-05 18.8 -0.5 14 51-64 32-45 (50)
58 cd06171 Sigma70_r4 Sigma70, re 48.7 21 0.00046 15.0 1.9 32 27-63 11-42 (55)
59 PRK07539 NADH dehydrogenase su 48.0 28 0.0006 19.5 2.7 31 34-64 27-57 (154)
60 PF05848 CtsR: Firmicute trans 47.3 7.5 0.00016 22.1 0.3 16 49-64 27-42 (152)
61 PF00196 GerE: Bacterial regul 46.7 15 0.00033 16.7 1.3 31 26-62 3-33 (58)
62 PF08281 Sigma70_r4_2: Sigma-7 45.5 24 0.00053 15.6 1.9 30 28-62 12-41 (54)
63 PRK07571 bidirectional hydroge 44.0 36 0.00077 19.6 2.7 25 40-64 47-71 (169)
64 PF01257 2Fe-2S_thioredx: Thio 42.0 22 0.00048 19.6 1.7 31 34-64 18-48 (145)
65 PF07750 GcrA: GcrA cell cycle 41.1 63 0.0014 18.4 3.4 31 26-61 2-33 (162)
66 PF13404 HTH_AsnC-type: AsnC-t 39.7 6.8 0.00015 17.2 -0.5 14 50-63 20-33 (42)
67 cd00569 HTH_Hin_like Helix-tur 39.0 27 0.00059 12.9 2.7 31 27-62 6-36 (42)
68 PF00325 Crp: Bacterial regula 38.9 8 0.00017 16.2 -0.3 14 49-62 4-17 (32)
69 PF13443 HTH_26: Cro/C1-type H 38.6 40 0.00087 15.3 2.1 29 35-63 27-56 (63)
70 TIGR00721 tfx DNA-binding prot 37.7 43 0.00093 18.7 2.4 34 24-63 4-37 (137)
71 cd08313 Death_TNFR1 Death doma 36.6 14 0.00031 18.6 0.3 15 50-64 14-28 (80)
72 PRK06759 RNA polymerase factor 35.1 42 0.00092 17.9 2.1 15 49-63 124-138 (154)
73 PF07954 DUF1689: Protein of u 35.0 70 0.0015 18.2 3.0 23 35-57 4-26 (152)
74 PRK04217 hypothetical protein; 34.4 47 0.001 17.8 2.1 35 24-63 40-74 (110)
75 PF10078 DUF2316: Uncharacteri 33.9 14 0.00031 19.1 0.1 25 34-62 14-38 (89)
76 PF13730 HTH_36: Helix-turn-he 33.6 18 0.0004 16.1 0.4 18 46-63 24-41 (55)
77 TIGR02989 Sig-70_gvs1 RNA poly 33.0 51 0.0011 17.7 2.2 15 49-63 129-143 (159)
78 TIGR03879 near_KaiC_dom probab 32.5 5.8 0.00012 19.8 -1.5 25 39-63 24-48 (73)
79 TIGR02959 SigZ RNA polymerase 32.1 51 0.0011 18.2 2.2 14 49-62 118-131 (170)
80 KOG0041|consensus 31.6 1E+02 0.0022 18.8 3.4 37 26-62 92-133 (244)
81 cd08306 Death_FADD Fas-associa 29.8 19 0.0004 18.2 0.1 13 51-63 17-29 (86)
82 smart00421 HTH_LUXR helix_turn 29.5 57 0.0012 13.9 2.4 30 27-62 4-33 (58)
83 PF12200 DUF3597: Domain of un 29.5 51 0.0011 18.3 1.8 17 45-61 83-99 (127)
84 PRK12529 RNA polymerase sigma 29.3 62 0.0014 18.0 2.2 14 49-62 145-158 (178)
85 PRK09413 IS2 repressor TnpA; R 29.2 98 0.0021 16.4 3.6 36 24-63 10-45 (121)
86 TIGR03209 P21_Cbot clostridium 29.1 96 0.0021 16.4 2.9 15 50-64 126-140 (142)
87 PF06056 Terminase_5: Putative 29.0 6.7 0.00014 18.5 -1.5 15 49-63 15-29 (58)
88 PRK09648 RNA polymerase sigma 28.2 64 0.0014 18.0 2.1 14 49-62 157-170 (189)
89 PRK09646 RNA polymerase sigma 27.1 89 0.0019 17.6 2.6 15 49-63 160-174 (194)
90 PRK07037 extracytoplasmic-func 26.9 74 0.0016 17.2 2.2 15 49-63 127-141 (163)
91 PRK09047 RNA polymerase factor 26.7 75 0.0016 17.1 2.2 14 50-63 125-138 (161)
92 PF13412 HTH_24: Winged helix- 26.2 52 0.0011 14.1 1.3 29 30-62 4-32 (48)
93 PRK09642 RNA polymerase sigma 26.1 79 0.0017 17.1 2.2 14 50-63 125-138 (160)
94 PRK12537 RNA polymerase sigma 25.8 1.1E+02 0.0023 17.1 2.8 15 49-63 151-165 (182)
95 PRK12541 RNA polymerase sigma 25.5 63 0.0014 17.5 1.8 13 50-62 131-143 (161)
96 PRK12526 RNA polymerase sigma 25.2 80 0.0017 18.1 2.2 15 49-63 171-185 (206)
97 TIGR02937 sigma70-ECF RNA poly 24.9 79 0.0017 16.2 2.0 15 49-63 128-142 (158)
98 PF13309 HTH_22: HTH domain 24.9 93 0.002 14.7 2.1 37 27-63 21-58 (64)
99 PRK12512 RNA polymerase sigma 24.9 86 0.0019 17.4 2.3 15 49-63 149-163 (184)
100 cd08319 Death_RAIDD Death doma 24.9 26 0.00056 17.8 0.1 13 51-63 17-29 (83)
101 PRK09645 RNA polymerase sigma 24.8 97 0.0021 16.9 2.4 13 50-62 137-149 (173)
102 TIGR02999 Sig-70_X6 RNA polyme 24.5 84 0.0018 17.3 2.2 15 49-63 152-166 (183)
103 PF08765 Mor: Mor transcriptio 24.5 17 0.00038 19.0 -0.6 16 49-64 74-89 (108)
104 PRK09652 RNA polymerase sigma 24.3 78 0.0017 17.2 2.0 14 50-63 147-160 (182)
105 TIGR02885 spore_sigF RNA polym 24.2 78 0.0017 18.4 2.1 15 49-63 201-215 (231)
106 PF14174 YycC: YycC-like prote 24.0 46 0.001 15.5 0.8 18 46-63 7-24 (53)
107 TIGR02985 Sig70_bacteroi1 RNA 24.0 88 0.0019 16.5 2.1 15 49-63 131-145 (161)
108 PRK15372 pathogenicity island 23.8 66 0.0014 20.1 1.7 31 26-56 11-41 (292)
109 TIGR02952 Sig70_famx2 RNA poly 23.7 86 0.0019 17.0 2.1 14 49-62 140-153 (170)
110 TIGR02954 Sig70_famx3 RNA poly 23.7 99 0.0021 16.9 2.3 15 49-63 137-151 (169)
111 COG5126 FRQ1 Ca2+-binding prot 23.6 1E+02 0.0022 17.7 2.3 38 22-59 9-51 (160)
112 PRK12515 RNA polymerase sigma 23.4 93 0.002 17.4 2.2 13 50-62 150-162 (189)
113 cd08318 Death_NMPP84 Death dom 23.3 29 0.00063 17.5 0.1 31 26-63 4-34 (86)
114 PRK12373 NADH dehydrogenase su 23.0 1.2E+02 0.0025 20.2 2.8 25 40-64 48-72 (400)
115 PF06918 DUF1280: Protein of u 22.8 1.9E+02 0.0041 17.5 4.3 39 23-61 61-103 (224)
116 PRK12514 RNA polymerase sigma 22.7 1.2E+02 0.0027 16.6 2.6 15 49-63 147-161 (179)
117 PRK12534 RNA polymerase sigma 22.6 1.4E+02 0.0029 16.6 2.8 15 49-63 155-169 (187)
118 PF04552 Sigma54_DBD: Sigma-54 22.5 29 0.00062 19.8 0.0 22 43-64 45-66 (160)
119 KOG1691|consensus 22.5 94 0.002 18.7 2.1 17 28-44 193-209 (210)
120 PRK00118 putative DNA-binding 22.5 1.1E+02 0.0023 16.3 2.2 31 27-62 18-48 (104)
121 PF10410 DnaB_bind: DnaB-helic 22.1 84 0.0018 14.0 1.6 13 51-63 46-58 (59)
122 TIGR02983 SigE-fam_strep RNA p 22.0 96 0.0021 16.7 2.1 15 49-63 128-142 (162)
123 PF12793 SgrR_N: Sugar transpo 22.0 64 0.0014 17.3 1.3 31 31-63 5-35 (115)
124 cd08779 Death_PIDD Death Domai 21.9 34 0.00074 17.3 0.2 13 51-63 17-29 (86)
125 PRK11924 RNA polymerase sigma 21.8 1E+02 0.0023 16.6 2.2 15 49-63 143-157 (179)
126 PRK12530 RNA polymerase sigma 21.5 98 0.0021 17.4 2.1 15 49-63 152-166 (189)
127 PRK08215 sporulation sigma fac 21.4 93 0.002 18.6 2.0 33 26-63 209-241 (258)
128 PRK09639 RNA polymerase sigma 21.3 99 0.0021 16.7 2.0 13 50-62 130-142 (166)
129 cd08315 Death_TRAILR_DR4_DR5 D 21.2 98 0.0021 16.0 1.8 15 49-63 21-35 (96)
130 PF13518 HTH_28: Helix-turn-he 21.1 38 0.00081 14.6 0.2 16 49-64 14-29 (52)
131 PF05269 Phage_CII: Bacterioph 21.0 55 0.0012 17.0 0.9 16 49-64 25-40 (91)
132 PRK12511 RNA polymerase sigma 20.8 1.1E+02 0.0024 17.2 2.2 14 49-62 129-142 (182)
133 PRK12547 RNA polymerase sigma 20.8 1.1E+02 0.0024 16.7 2.1 14 49-62 130-143 (164)
134 COG3711 BglG Transcriptional a 20.7 1.2E+02 0.0026 19.8 2.5 32 30-64 5-36 (491)
135 cd08784 Death_DRs Death Domain 20.2 39 0.00085 16.7 0.2 15 49-63 13-27 (79)
136 PRK10430 DNA-binding transcrip 20.0 1.1E+02 0.0023 17.8 2.0 38 26-64 158-195 (239)
No 1
>KOG0488|consensus
Probab=99.55 E-value=9.4e-15 Score=89.23 Aligned_cols=47 Identities=49% Similarity=0.704 Sum_probs=45.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+|+|+.||.||..|+.+||+.|++.+|++..+|++||..|||+++||
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQV 216 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQV 216 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhH
Confidence 77888899999999999999999999999999999999999999997
No 2
>KOG0842|consensus
Probab=99.42 E-value=2.1e-13 Score=83.00 Aligned_cols=48 Identities=42% Similarity=0.612 Sum_probs=45.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 17 FRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 17 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+++||.|..||..|..+||+.|..++|++.++|++||..|+||+.||
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQV 197 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQV 197 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchhe
Confidence 357778899999999999999999999999999999999999999998
No 3
>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=99.42 E-value=6.2e-13 Score=63.84 Aligned_cols=44 Identities=27% Similarity=0.357 Sum_probs=42.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHcCCCCcCC
Q psy13127 21 KRIRTAFSPSQLLKLEHAFEKNHY----VVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 21 rr~Rt~~t~~q~~~Le~~F~~~~~----~~~~~r~~La~~l~l~~~qV 64 (64)
+|.||.||..|+..|+..|+.+.| |+..++.+||..|||++.+|
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vv 49 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVF 49 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHe
Confidence 678999999999999999999999 99999999999999998765
No 4
>KOG2251|consensus
Probab=99.38 E-value=5.9e-13 Score=77.71 Aligned_cols=47 Identities=40% Similarity=0.507 Sum_probs=45.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
|+.||.||.|+..|+.+||..|.+..||++..|++||.+|+|++.+|
T Consensus 35 RkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrV 81 (228)
T KOG2251|consen 35 RKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRV 81 (228)
T ss_pred hhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhh
Confidence 88999999999999999999999999999999999999999999876
No 5
>KOG0484|consensus
Probab=99.38 E-value=1.1e-13 Score=73.00 Aligned_cols=49 Identities=39% Similarity=0.579 Sum_probs=45.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 16 PFRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 16 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
..+++||-||.||..|+.+||+.|...+||++.+|++||.++.|++++|
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARV 61 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARV 61 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHH
Confidence 3488899999999999999999999999999999999999999999764
No 6
>KOG0487|consensus
Probab=99.36 E-value=1.4e-12 Score=79.49 Aligned_cols=49 Identities=33% Similarity=0.522 Sum_probs=46.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 16 PFRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 16 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
..++.||+|..||..|+.+||+.|-.|.|++.+.|.+|+..|+|+++||
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQV 279 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQV 279 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhe
Confidence 3488899999999999999999999999999999999999999999998
No 7
>KOG0843|consensus
Probab=99.34 E-value=2e-12 Score=73.73 Aligned_cols=46 Identities=85% Similarity=1.174 Sum_probs=44.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 19 KPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 19 ~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+.+|.||.||..|+.-||..|+.++|....+|.+||..|+|++.||
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQV 146 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQV 146 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHh
Confidence 8889999999999999999999999999999999999999999987
No 8
>KOG0489|consensus
Probab=99.31 E-value=8.2e-13 Score=79.21 Aligned_cols=47 Identities=47% Similarity=0.656 Sum_probs=44.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+.||.||.||..|+.+||+.|..|+|++...|.+||..|+|+|+||
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQI 203 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQI 203 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHH
Confidence 45788999999999999999999999999999999999999999997
No 9
>KOG0850|consensus
Probab=99.31 E-value=2.3e-12 Score=75.70 Aligned_cols=47 Identities=40% Similarity=0.581 Sum_probs=44.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+|-|+.||.|+..||..|++.|++.+|+..++|.+||..|||+..||
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQV 166 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQV 166 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHh
Confidence 66778899999999999999999999999999999999999999987
No 10
>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=99.26 E-value=5.3e-12 Score=60.00 Aligned_cols=44 Identities=48% Similarity=0.622 Sum_probs=41.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 21 rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
|+.|+.||..|+..|+..|..++||+..++..||..+||+..+|
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V 44 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQV 44 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhcccccccccccccccccccccc
Confidence 56899999999999999999999999999999999999998765
No 11
>KOG0492|consensus
Probab=99.18 E-value=3.6e-11 Score=70.04 Aligned_cols=47 Identities=43% Similarity=0.640 Sum_probs=44.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+..|+.||.||..|+..||+.|..++|+++.+|.+++..|.|++.||
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqV 188 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQV 188 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhhe
Confidence 55577899999999999999999999999999999999999999987
No 12
>KOG0485|consensus
Probab=99.17 E-value=3.1e-11 Score=70.76 Aligned_cols=47 Identities=49% Similarity=0.681 Sum_probs=44.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.++++.||+|+..|+..||..|+..+|++..+|..||.+|.|+|.||
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQV 148 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQV 148 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhh
Confidence 36778899999999999999999999999999999999999999987
No 13
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.10 E-value=2e-10 Score=54.14 Aligned_cols=43 Identities=49% Similarity=0.719 Sum_probs=40.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 22 RIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 22 r~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+.|+.|+..|+..|+..|..++||+..++..||..+||+..||
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV 44 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQV 44 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHH
Confidence 4678899999999999999999999999999999999998765
No 14
>KOG0494|consensus
Probab=99.07 E-value=3.6e-10 Score=67.86 Aligned_cols=45 Identities=38% Similarity=0.527 Sum_probs=41.0
Q ss_pred CCC-CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 20 PKR-IRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 20 ~rr-~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+|| .||.||..|+.+||+.|...+||+...|+-||.++.|++.+|
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRI 185 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRI 185 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhh
Confidence 344 499999999999999999999999999999999999998754
No 15
>KOG0493|consensus
Probab=99.05 E-value=4e-10 Score=67.74 Aligned_cols=44 Identities=45% Similarity=0.715 Sum_probs=41.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 21 rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+|.||.||.+|+..|...|+.|+|++...|.+||..|+|.+.||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQI 290 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQI 290 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHh
Confidence 46799999999999999999999999999999999999999886
No 16
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.05 E-value=4.4e-10 Score=53.32 Aligned_cols=43 Identities=53% Similarity=0.742 Sum_probs=40.3
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 22 RIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 22 r~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+.++.|+..|+..|+..|..++||+..++..||..+||+..||
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV 44 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQV 44 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHH
Confidence 4678999999999999999999999999999999999998776
No 17
>KOG0486|consensus
Probab=99.04 E-value=1.4e-10 Score=70.87 Aligned_cols=47 Identities=36% Similarity=0.524 Sum_probs=44.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+|+||.||.||..|+.+||..|++|.||+..+|++||+-++|++.+|
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rv 156 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARV 156 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhh
Confidence 47888999999999999999999999999999999999999999875
No 18
>KOG0848|consensus
Probab=99.03 E-value=9.1e-11 Score=70.49 Aligned_cols=47 Identities=30% Similarity=0.530 Sum_probs=44.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
|.+.+.|.+||+.|+.+||++|..++|+++..+.+||..|+|+|+||
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQV 243 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQV 243 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhh
Confidence 56667899999999999999999999999999999999999999997
No 19
>KOG0491|consensus
Probab=98.91 E-value=1.3e-10 Score=65.68 Aligned_cols=46 Identities=46% Similarity=0.699 Sum_probs=43.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 19 KPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 19 ~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+.++.||+|+..|+..|++.|+..+|++.+++.+||+.|+|++.||
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QV 144 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQV 144 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHH
Confidence 4566799999999999999999999999999999999999999886
No 20
>KOG0849|consensus
Probab=98.77 E-value=1.4e-08 Score=63.36 Aligned_cols=48 Identities=40% Similarity=0.518 Sum_probs=44.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 17 FRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 17 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.++.++.||.|+..|+..|+..|+.++||+...|++||..+++++.+|
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~ri 220 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRV 220 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHH
Confidence 367788899999999999999999999999999999999999998654
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.66 E-value=7.3e-08 Score=54.30 Aligned_cols=47 Identities=30% Similarity=0.393 Sum_probs=42.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+..+++|++-|.+|+..|+..|+.++||+..+|.+|+..|+|++.-|
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksV 95 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSV 95 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhh
Confidence 45667788889999999999999999999999999999999998654
No 22
>KOG0490|consensus
Probab=98.66 E-value=2e-08 Score=58.57 Aligned_cols=48 Identities=38% Similarity=0.275 Sum_probs=44.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 17 FRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 17 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
..+.++.|+.|+.+|+.+|++.|+..+||+...++.||..+++++..|
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rV 104 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRV 104 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeee
Confidence 357788999999999999999999999999999999999999998765
No 23
>KOG0844|consensus
Probab=98.62 E-value=1.5e-08 Score=62.14 Aligned_cols=47 Identities=38% Similarity=0.597 Sum_probs=43.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+-||.||.||.+|+..||+.|-+..|.+.+.|-+||..|||++..|
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTI 225 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTI 225 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCccee
Confidence 45688999999999999999999999999999999999999999754
No 24
>KOG3802|consensus
Probab=98.55 E-value=1.5e-07 Score=59.19 Aligned_cols=47 Identities=26% Similarity=0.275 Sum_probs=43.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.++||+||.+....+..||..|.+|+.|+..+...||.+|+|....|
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVV 338 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVV 338 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceE
Confidence 46788999999999999999999999999999999999999987654
No 25
>KOG0483|consensus
Probab=98.23 E-value=1.3e-06 Score=50.87 Aligned_cols=44 Identities=27% Similarity=0.375 Sum_probs=40.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 21 rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+++.+|+..|...||..|+.+.++....+..||..|||.++||
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQV 94 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQV 94 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHH
Confidence 34566899999999999999999999999999999999999987
No 26
>KOG2252|consensus
Probab=97.98 E-value=9.3e-06 Score=53.03 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=41.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 19 KPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 19 ~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+.++.|.+||+.|...|...|+.+++|+......|+.+|+|....|
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV 464 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTV 464 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHH
Confidence 4566799999999999999999999999999999999999976543
No 27
>KOG0847|consensus
Probab=97.86 E-value=1.4e-05 Score=47.51 Aligned_cols=47 Identities=43% Similarity=0.698 Sum_probs=42.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+++-.|..|+..|+..||..|+..+|+-.++|.+||..+|+++.||
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqv 211 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQV 211 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHH
Confidence 34444688999999999999999999999999999999999999875
No 28
>KOG4577|consensus
Probab=97.62 E-value=8.2e-05 Score=45.83 Aligned_cols=47 Identities=26% Similarity=0.281 Sum_probs=42.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
...+|.||.+|..|+..|...+...+.|..+.|+.|+..+||--+.|
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVV 211 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVV 211 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeeh
Confidence 35678899999999999999999999999999999999999987654
No 29
>KOG0774|consensus
Probab=97.21 E-value=0.00049 Score=41.98 Aligned_cols=45 Identities=27% Similarity=0.352 Sum_probs=39.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 20 PKRIRTAFSPSQLLKLEHAFE---KNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 20 ~rr~Rt~~t~~q~~~Le~~F~---~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+|+|..|+..--..|...|. .|+||+-.++++||.+.|++-.||
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQv 235 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQV 235 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhh
Confidence 356777899999999999997 488999999999999999998876
No 30
>KOG0775|consensus
Probab=97.16 E-value=0.0008 Score=41.16 Aligned_cols=38 Identities=29% Similarity=0.344 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 27 FSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 27 ~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
|...-...|...|..++||+..++.+||..+||+..||
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQV 220 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQV 220 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhh
Confidence 55666788999999999999999999999999999887
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=97.07 E-value=0.00015 Score=32.28 Aligned_cols=24 Identities=29% Similarity=0.464 Sum_probs=18.8
Q ss_pred hcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 41 KNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 41 ~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.++||+..++..||..+|++..||
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi 30 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQI 30 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHH
Confidence 479999999999999999998775
No 32
>KOG1168|consensus
Probab=96.35 E-value=0.003 Score=39.15 Aligned_cols=45 Identities=24% Similarity=0.302 Sum_probs=39.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 19 KPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 19 ~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
-++|+||.+-.-....||..|...+-|+.+....+|.+|.|....
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNV 352 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNV 352 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhce
Confidence 456788898888899999999999999999999999999987654
No 33
>KOG0490|consensus
Probab=96.21 E-value=0.0053 Score=35.76 Aligned_cols=46 Identities=37% Similarity=0.512 Sum_probs=42.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 18 RKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 18 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
.+.++.|+.+...|+..+...|..+.+|+...+..|+..+|+++..
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~ 196 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERV 196 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhh
Confidence 5677789999999999999999999999999999999999998754
No 34
>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=94.34 E-value=0.042 Score=25.81 Aligned_cols=36 Identities=19% Similarity=0.276 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCCc
Q psy13127 27 FSPSQLLKLEHAFEKNHY--VVGAERKQLAQSLSLTET 62 (64)
Q Consensus 27 ~t~~q~~~Le~~F~~~~~--~~~~~r~~La~~l~l~~~ 62 (64)
+|+.|...|...++...| |-...-.+||..||++..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~s 38 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKS 38 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHH
Confidence 478899999999998887 555566789999999864
No 35
>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=94.10 E-value=0.12 Score=23.99 Aligned_cols=39 Identities=15% Similarity=0.400 Sum_probs=28.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 21 KRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 21 rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+++|..+|-.+...+-..++.+. ....+|..+|++..+|
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv 39 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTV 39 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHH
Confidence 46788999999998888888876 5678999999988764
No 36
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=91.48 E-value=0.26 Score=28.84 Aligned_cols=37 Identities=22% Similarity=0.312 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCCc
Q psy13127 26 AFSPSQLLKLEHAFEKNHY--VVGAERKQLAQSLSLTET 62 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~~~~--~~~~~r~~La~~l~l~~~ 62 (64)
.+|+.|+..|...|....| |-...-.+||..+|++..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISks 193 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKS 193 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHH
Confidence 6999999999999998886 666666799999999863
No 37
>KOG1146|consensus
Probab=86.41 E-value=0.87 Score=33.61 Aligned_cols=45 Identities=20% Similarity=0.197 Sum_probs=40.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 20 PKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 20 ~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+..|+.++..|+..+...|....|+...+.+.|...++++.+.|
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i 947 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVI 947 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchh
Confidence 355799999999999999999999999999999999999988654
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=83.65 E-value=0.54 Score=22.36 Aligned_cols=33 Identities=15% Similarity=0.222 Sum_probs=22.4
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 32 LLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 32 ~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+..|+..|....++.-.+-..|..+.+|+..||
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqV 42 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQV 42 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHH
Confidence 356999999999998888889999999987765
No 39
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=77.94 E-value=1 Score=19.98 Aligned_cols=34 Identities=15% Similarity=0.336 Sum_probs=14.6
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 25 TAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 25 t~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
..+|..+...++...+.+ ....++|..||.+...
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sT 36 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRST 36 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHH
Confidence 356777788887765544 3566899999987643
No 40
>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=73.24 E-value=2.8 Score=18.67 Aligned_cols=33 Identities=9% Similarity=0.252 Sum_probs=22.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
..++.+...+...|-.+ ..-.++|..+|++...
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~ 36 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRST 36 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHH
Confidence 35677778888777333 2456899999998753
No 41
>PF15063 TC1: Thyroid cancer protein 1
Probab=72.23 E-value=4.5 Score=20.46 Aligned_cols=50 Identities=20% Similarity=0.328 Sum_probs=30.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHH
Q psy13127 6 RPDIPGFLLQPFRKPKRIRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQ 55 (64)
Q Consensus 6 ~~~~~~~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~ 55 (64)
+|+.+|.......+++-.--.|..-.+..|.+.|+..=-....+|..+--
T Consensus 13 ~Ps~~g~~~dt~~RKkasaNIFe~vn~~qlqrLF~~sGD~kAEeRA~iI~ 62 (79)
T PF15063_consen 13 SPSVHGYKFDTASRKKASANIFENVNLDQLQRLFQKSGDKKAEERARIIW 62 (79)
T ss_pred cCCCCCCCcchHHhhhhhhhhhhccCHHHHHHHHHHccchhHHHHHHHHH
Confidence 44455555443222222334577777788889999887777777776543
No 42
>KOG0773|consensus
Probab=68.09 E-value=11 Score=23.63 Aligned_cols=42 Identities=19% Similarity=0.210 Sum_probs=31.9
Q ss_pred CCCCCCHHHHHHHHHHH-h--hcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 23 IRTAFSPSQLLKLEHAF-E--KNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 23 ~Rt~~t~~q~~~Le~~F-~--~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+..+.......|+... + ..+||+..++..||..+||+..||
T Consensus 242 ~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv 286 (342)
T KOG0773|consen 242 PQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQV 286 (342)
T ss_pred CCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccC
Confidence 34466677777776553 2 267999999999999999999876
No 43
>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=67.63 E-value=6.3 Score=18.83 Aligned_cols=36 Identities=19% Similarity=0.378 Sum_probs=20.6
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 22 RIRTAFSPSQLLKLEHAF-EKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 22 r~Rt~~t~~q~~~Le~~F-~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
+.|..||..+...+-... ... .....+|..+|++..
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~ 38 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPS 38 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccc
Confidence 356788998888666555 333 356788999988754
No 44
>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=67.06 E-value=7.5 Score=16.78 Aligned_cols=16 Identities=31% Similarity=0.522 Sum_probs=13.0
Q ss_pred CCCHHHHHHHHHHHhh
Q psy13127 26 AFSPSQLLKLEHAFEK 41 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~ 41 (64)
.||..|+..|+.-...
T Consensus 2 ~FT~~Ql~~L~~Qi~a 17 (37)
T PF08880_consen 2 PFTPAQLQELRAQILA 17 (37)
T ss_pred CCCHHHHHHHHHHHHH
Confidence 6999999999876543
No 45
>PRK13558 bacterio-opsin activator; Provisional
Probab=66.91 E-value=8.8 Score=25.81 Aligned_cols=38 Identities=21% Similarity=0.384 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCCc
Q psy13127 25 TAFSPSQLLKLEHAFEKNHY--VVGAERKQLAQSLSLTET 62 (64)
Q Consensus 25 t~~t~~q~~~Le~~F~~~~~--~~~~~r~~La~~l~l~~~ 62 (64)
..+|..|...|+..+....| |-...-.+||..||++..
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~ 645 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRS 645 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHH
Confidence 46999999999999999987 666677899999999864
No 46
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=65.88 E-value=4.6 Score=18.86 Aligned_cols=30 Identities=30% Similarity=0.435 Sum_probs=20.1
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 30 SQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 30 ~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
.|+.-|+-.+. +.+.+.. +||..+|+++..
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rt 35 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERT 35 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHH
Confidence 35566666667 6666555 799999998753
No 47
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.18 E-value=13 Score=19.40 Aligned_cols=35 Identities=20% Similarity=0.346 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCC
Q psy13127 27 FSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61 (64)
Q Consensus 27 ~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~ 61 (64)
..+.|...-...|+.|--.+.-..+++|..||.++
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~ 37 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTE 37 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCH
Confidence 45667766666677666666666778999998876
No 48
>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=60.62 E-value=6.6 Score=17.25 Aligned_cols=32 Identities=9% Similarity=0.309 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
.++..+...+...+.... ...++|..+|++..
T Consensus 5 ~~~~~~~~~i~~l~~~G~-----si~~IA~~~gvsr~ 36 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEGM-----SIAEIAKQFGVSRS 36 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HH
T ss_pred CCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHH
Confidence 355655666666666552 46689999998764
No 49
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=59.05 E-value=20 Score=20.59 Aligned_cols=36 Identities=14% Similarity=0.173 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 29 PSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 29 ~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
..-+..|...+...-|.+......+|..||++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 345567777788777999999999999999997654
No 50
>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=55.30 E-value=38 Score=19.40 Aligned_cols=37 Identities=14% Similarity=0.241 Sum_probs=29.9
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCC
Q psy13127 23 IRTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTE 61 (64)
Q Consensus 23 ~Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~ 61 (64)
+...+|.+++.++...-..+ |....+..||.+.||+.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~ 118 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSP 118 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCH
Confidence 45789999999988766555 55678899999999986
No 51
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=52.88 E-value=17 Score=19.69 Aligned_cols=38 Identities=24% Similarity=0.239 Sum_probs=29.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 25 TAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 25 t~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
.-.+..-..+|+..|-..+---..-|.+||.+.|+.+-
T Consensus 94 yflsesgmeelqdrfmns~st~yrwrke~a~kfgvr~p 131 (143)
T PRK15183 94 YFLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREP 131 (143)
T ss_pred hhhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCC
Confidence 34567778889999987776556668899999998763
No 52
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=52.64 E-value=16 Score=20.42 Aligned_cols=34 Identities=15% Similarity=0.250 Sum_probs=24.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 24 RTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 24 Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
...+++.|...|... ..+. ...++|..||++...
T Consensus 4 ~~~Lt~rqreVL~lr-~~Gl-----Tq~EIAe~LGiS~~t 37 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERGL-----TQQEIADILGTSRAN 37 (141)
T ss_pred ccCCCHHHHHHHHHH-HcCC-----CHHHHHHHHCCCHHH
Confidence 346788898888773 3232 566899999998743
No 53
>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=52.04 E-value=12 Score=16.74 Aligned_cols=13 Identities=31% Similarity=0.526 Sum_probs=9.2
Q ss_pred HHHHHHHcCCCCc
Q psy13127 50 RKQLAQSLSLTET 62 (64)
Q Consensus 50 r~~La~~l~l~~~ 62 (64)
..+||..++++.+
T Consensus 18 ~~eLa~~l~vS~r 30 (55)
T PF08279_consen 18 AKELAEELGVSRR 30 (55)
T ss_dssp HHHHHHHCTS-HH
T ss_pred HHHHHHHhCCCHH
Confidence 4478999998865
No 54
>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=51.17 E-value=5 Score=19.28 Aligned_cols=15 Identities=27% Similarity=0.505 Sum_probs=12.0
Q ss_pred HHHHHHHcCCCCcCC
Q psy13127 50 RKQLAQSLSLTETQF 64 (64)
Q Consensus 50 r~~La~~l~l~~~qV 64 (64)
-.+||..||+++.+|
T Consensus 25 lkdIA~~Lgvs~~tI 39 (60)
T PF10668_consen 25 LKDIAEKLGVSESTI 39 (60)
T ss_pred HHHHHHHHCCCHHHH
Confidence 457999999998765
No 55
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=49.70 E-value=26 Score=19.78 Aligned_cols=32 Identities=19% Similarity=0.216 Sum_probs=23.3
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 33 LKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 33 ~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
..|...=+..-|.+......+|..||++..+|
T Consensus 27 ~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V 58 (156)
T PRK05988 27 PILHAIQDEFGYVPEDAVPVIAEALNLSRAEV 58 (156)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHH
Confidence 34433334456899999999999999998654
No 56
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=49.64 E-value=25 Score=19.47 Aligned_cols=31 Identities=19% Similarity=0.167 Sum_probs=22.4
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 34 KLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 34 ~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.|...=+.--|.+......+|..||++..+|
T Consensus 21 ~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 21 ALMIAQEQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 3333333445899999999999999997654
No 57
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=49.45 E-value=3.9 Score=18.84 Aligned_cols=14 Identities=36% Similarity=0.596 Sum_probs=10.6
Q ss_pred HHHHHHcCCCCcCC
Q psy13127 51 KQLAQSLSLTETQF 64 (64)
Q Consensus 51 ~~La~~l~l~~~qV 64 (64)
.+||..+|+++.||
T Consensus 32 ~~La~~~gi~~~qV 45 (50)
T PF06971_consen 32 QELAEALGITPAQV 45 (50)
T ss_dssp HHHHHHHTS-HHHH
T ss_pred HHHHHHHCCCHHHh
Confidence 47899999988775
No 58
>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=48.68 E-value=21 Score=14.97 Aligned_cols=32 Identities=9% Similarity=0.187 Sum_probs=18.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 27 FSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 27 ~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
++..+...+...+..+ .....+|..+|++...
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~ 42 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRST 42 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHH
Confidence 4555666665544322 2455778888887654
No 59
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=47.96 E-value=28 Score=19.47 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=22.6
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 34 KLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 34 ~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.|...=+.--|.+......+|..+|++..+|
T Consensus 27 ~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v 57 (154)
T PRK07539 27 ALKIVQEQRGWVPDEAIEAVADYLGMPAIDV 57 (154)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 3333333456888999999999999998654
No 60
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=47.26 E-value=7.5 Score=22.10 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=12.5
Q ss_pred HHHHHHHHcCCCCcCC
Q psy13127 49 ERKQLAQSLSLTETQF 64 (64)
Q Consensus 49 ~r~~La~~l~l~~~qV 64 (64)
.|.+||.+++|-++||
T Consensus 27 qR~eLA~~F~CvPSQI 42 (152)
T PF05848_consen 27 QRNELAERFNCVPSQI 42 (152)
T ss_dssp -HHHHHHHTTS-THHH
T ss_pred eHHHHHHHhCCchhhh
Confidence 5789999999999885
No 61
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=46.70 E-value=15 Score=16.72 Aligned_cols=31 Identities=19% Similarity=0.296 Sum_probs=18.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
.+|+.+...|.....-. ...++|..+++++.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~ 33 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEK 33 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchh
Confidence 46777777776655544 35567777776653
No 62
>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=45.46 E-value=24 Score=15.61 Aligned_cols=30 Identities=17% Similarity=0.226 Sum_probs=15.5
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 28 SPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 28 t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
++.+...+...| .....-.++|..+|++..
T Consensus 12 ~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~ 41 (54)
T PF08281_consen 12 PERQREIFLLRY-----FQGMSYAEIAEILGISES 41 (54)
T ss_dssp -HHHHHHHHHHH-----TS---HHHHHHHCTS-HH
T ss_pred CHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHH
Confidence 344444444333 333467789999998864
No 63
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=44.00 E-value=36 Score=19.60 Aligned_cols=25 Identities=20% Similarity=0.122 Sum_probs=20.0
Q ss_pred hhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 40 EKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 40 ~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+..-|.+......+|..||++..+|
T Consensus 47 ~~~GyIp~e~~~~iA~~l~v~~a~V 71 (169)
T PRK07571 47 ELFGYLERDLLLYVARQLKLPLSRV 71 (169)
T ss_pred HHcCCCCHHHHHHHHHHhCcCHHHH
Confidence 3455888899999999999987653
No 64
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=42.05 E-value=22 Score=19.63 Aligned_cols=31 Identities=16% Similarity=0.307 Sum_probs=19.9
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 34 KLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 34 ~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.|...=+..-|.+......+|..+|++..+|
T Consensus 18 ~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v 48 (145)
T PF01257_consen 18 ILHEVQEEYGYIPEEALEEIAEALGIPPAEV 48 (145)
T ss_dssp HHHHHHHHHSS--HHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHCCCHHHH
Confidence 3443334455888999999999999987653
No 65
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=41.14 E-value=63 Score=18.42 Aligned_cols=31 Identities=13% Similarity=0.361 Sum_probs=22.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcC-CCC
Q psy13127 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLS-LTE 61 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~-l~~ 61 (64)
.+|++.+..|...+.... .-.++|..|| ++.
T Consensus 2 ~Wtde~~~~L~~lw~~G~-----SasqIA~~lg~vsR 33 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL-----SASQIARQLGGVSR 33 (162)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCcch
Confidence 467888888888777654 4567888888 554
No 66
>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=39.65 E-value=6.8 Score=17.17 Aligned_cols=14 Identities=36% Similarity=0.544 Sum_probs=9.9
Q ss_pred HHHHHHHcCCCCcC
Q psy13127 50 RKQLAQSLSLTETQ 63 (64)
Q Consensus 50 r~~La~~l~l~~~q 63 (64)
-.+||..+|+++..
T Consensus 20 ~~~la~~lglS~~~ 33 (42)
T PF13404_consen 20 YAELAEELGLSEST 33 (42)
T ss_dssp HHHHHHHHTS-HHH
T ss_pred HHHHHHHHCcCHHH
Confidence 34789999998754
No 67
>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=38.95 E-value=27 Score=12.92 Aligned_cols=31 Identities=13% Similarity=0.343 Sum_probs=18.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 27 FSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 27 ~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
++..+...+...+.... ....+|..+|++..
T Consensus 6 ~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~ 36 (42)
T cd00569 6 LTPEQIEEARRLLAAGE-----SVAEIARRLGVSRS 36 (42)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHH
Confidence 45566555555555332 34467888887653
No 68
>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=38.89 E-value=8 Score=16.17 Aligned_cols=14 Identities=36% Similarity=0.534 Sum_probs=9.2
Q ss_pred HHHHHHHHcCCCCc
Q psy13127 49 ERKQLAQSLSLTET 62 (64)
Q Consensus 49 ~r~~La~~l~l~~~ 62 (64)
.+.++|..+|++..
T Consensus 4 tr~diA~~lG~t~E 17 (32)
T PF00325_consen 4 TRQDIADYLGLTRE 17 (32)
T ss_dssp -HHHHHHHHTS-HH
T ss_pred CHHHHHHHhCCcHH
Confidence 36688888888753
No 69
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=38.63 E-value=40 Score=15.31 Aligned_cols=29 Identities=10% Similarity=0.137 Sum_probs=15.5
Q ss_pred HHHHHhhc-CCCCHHHHHHHHHHcCCCCcC
Q psy13127 35 LEHAFEKN-HYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 35 Le~~F~~~-~~~~~~~r~~La~~l~l~~~q 63 (64)
+.+.+... ..++...-..||..||++..+
T Consensus 27 l~~~~~~~~~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 27 LSRILNGKPSNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp HHHHHTTT-----HHHHHHHHHHHT--HHH
T ss_pred HHHHHhcccccccHHHHHHHHHHcCCCHHH
Confidence 33444544 467888888899999887643
No 70
>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=37.69 E-value=43 Score=18.65 Aligned_cols=34 Identities=26% Similarity=0.303 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 24 RTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 24 Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
.+.++..|...+.... .+. ...++|..+|++...
T Consensus 4 ~~~Lte~qr~VL~Lr~-~Gl-----Tq~EIAe~LgiS~st 37 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KGL-----SQKEIAKELKTTRAN 37 (137)
T ss_pred cCCCCHHHHHHHHHHH-cCC-----CHHHHHHHHCcCHHH
Confidence 3567888888887642 222 566899999988653
No 71
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 a
Probab=36.62 E-value=14 Score=18.61 Aligned_cols=15 Identities=20% Similarity=0.501 Sum_probs=11.5
Q ss_pred HHHHHHHcCCCCcCC
Q psy13127 50 RKQLAQSLSLTETQF 64 (64)
Q Consensus 50 r~~La~~l~l~~~qV 64 (64)
=.+++..|||++.+|
T Consensus 14 wk~~~R~LGlse~~I 28 (80)
T cd08313 14 WKEFVRRLGLSDNEI 28 (80)
T ss_pred HHHHHHHcCCCHHHH
Confidence 347999999998653
No 72
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=35.10 E-value=42 Score=17.94 Aligned_cols=15 Identities=20% Similarity=0.111 Sum_probs=10.9
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 124 s~~EIA~~l~is~~t 138 (154)
T PRK06759 124 TMGEIALETEMTYYQ 138 (154)
T ss_pred CHHHHHHHHCCCHHH
Confidence 456788888887654
No 73
>PF07954 DUF1689: Protein of unknown function (DUF1689) ; InterPro: IPR012470 Family of fungal proteins with unknown function. A member of this family has been found to localise in the mitochondria [].
Probab=35.03 E-value=70 Score=18.21 Aligned_cols=23 Identities=22% Similarity=0.313 Sum_probs=18.9
Q ss_pred HHHHHhhcCCCCHHHHHHHHHHc
Q psy13127 35 LEHAFEKNHYVVGAERKQLAQSL 57 (64)
Q Consensus 35 Le~~F~~~~~~~~~~r~~La~~l 57 (64)
.....+.++.++..+|.+|+..+
T Consensus 4 av~FYEaD~~L~~~DR~eL~~~~ 26 (152)
T PF07954_consen 4 AVEFYEADQKLDHEDRLELAKDL 26 (152)
T ss_pred HHHHHHhhccCCHHHHHHHHHHH
Confidence 34567889999999999999876
No 74
>PRK04217 hypothetical protein; Provisional
Probab=34.36 E-value=47 Score=17.78 Aligned_cols=35 Identities=3% Similarity=0.028 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 24 RTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 24 Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
-..++..+...+...+...- ...++|..+|++...
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sT 74 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGT 74 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHH
Confidence 34567888777766554333 456789999988643
No 75
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=33.91 E-value=14 Score=19.12 Aligned_cols=25 Identities=24% Similarity=0.337 Sum_probs=15.7
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 34 KLEHAFEKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 34 ~Le~~F~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
+|..-|+..-+ ....+|..|+++..
T Consensus 14 ELq~nf~~~~l----s~~~ia~dL~~s~~ 38 (89)
T PF10078_consen 14 ELQANFELSGL----SLEQIAADLGTSPE 38 (89)
T ss_pred HHHHHHHHcCC----CHHHHHHHhCCCHH
Confidence 55555665544 35577888887764
No 76
>PF13730 HTH_36: Helix-turn-helix domain
Probab=33.64 E-value=18 Score=16.09 Aligned_cols=18 Identities=17% Similarity=0.266 Sum_probs=12.5
Q ss_pred CHHHHHHHHHHcCCCCcC
Q psy13127 46 VGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 46 ~~~~r~~La~~l~l~~~q 63 (64)
+.+....||..+|++...
T Consensus 24 ~~pS~~~la~~~g~s~~T 41 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRT 41 (55)
T ss_pred CCcCHHHHHHHHCcCHHH
Confidence 444566889999988643
No 77
>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=32.97 E-value=51 Score=17.68 Aligned_cols=15 Identities=27% Similarity=0.209 Sum_probs=9.3
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 129 ~~~eIA~~l~is~~t 143 (159)
T TIGR02989 129 SLTALAEQLGRTVNA 143 (159)
T ss_pred CHHHHHHHhCCCHHH
Confidence 445677777776543
No 78
>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=32.45 E-value=5.8 Score=19.80 Aligned_cols=25 Identities=20% Similarity=0.190 Sum_probs=15.6
Q ss_pred HhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 39 FEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 39 F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
|....|.......++|..+|+++..
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~T 48 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQT 48 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHH
Confidence 4433433334567899999988753
No 79
>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=32.13 E-value=51 Score=18.22 Aligned_cols=14 Identities=21% Similarity=0.489 Sum_probs=9.0
Q ss_pred HHHHHHHHcCCCCc
Q psy13127 49 ERKQLAQSLSLTET 62 (64)
Q Consensus 49 ~r~~La~~l~l~~~ 62 (64)
.-.++|..+|++..
T Consensus 118 s~~eIA~~lgis~~ 131 (170)
T TIGR02959 118 SQQEIAEKLGLSLS 131 (170)
T ss_pred CHHHHHHHHCCCHH
Confidence 34567777777654
No 80
>KOG0041|consensus
Probab=31.57 E-value=1e+02 Score=18.78 Aligned_cols=37 Identities=24% Similarity=0.380 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHcCCCCc
Q psy13127 26 AFSPSQLLKLEHAFEK-----NHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~-----~~~~~~~~r~~La~~l~l~~~ 62 (64)
-|+..|+..++..|.. +-|++.-+-..+..+||.+..
T Consensus 92 eFsrkqIk~~~~~Fk~yDe~rDgfIdl~ELK~mmEKLgapQT 133 (244)
T KOG0041|consen 92 EFSRKQIKDAESMFKQYDEDRDGFIDLMELKRMMEKLGAPQT 133 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHhCCchh
Confidence 4788899999999974 568888888888899987753
No 81
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=29.84 E-value=19 Score=18.21 Aligned_cols=13 Identities=46% Similarity=0.761 Sum_probs=10.4
Q ss_pred HHHHHHcCCCCcC
Q psy13127 51 KQLAQSLSLTETQ 63 (64)
Q Consensus 51 ~~La~~l~l~~~q 63 (64)
..||..||+++.+
T Consensus 17 k~laR~LGlse~~ 29 (86)
T cd08306 17 RKLARKLGLSETK 29 (86)
T ss_pred HHHHHHcCCCHHH
Confidence 4789999998754
No 82
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=29.55 E-value=57 Score=13.86 Aligned_cols=30 Identities=23% Similarity=0.348 Sum_probs=18.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 27 FSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 27 ~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
+++.+...+...+. +. ...++|..+|++..
T Consensus 4 l~~~e~~i~~~~~~-g~-----s~~eia~~l~is~~ 33 (58)
T smart00421 4 LTPREREVLRLLAE-GL-----TNKEIAERLGISEK 33 (58)
T ss_pred CCHHHHHHHHHHHc-CC-----CHHHHHHHHCCCHH
Confidence 46666666654332 21 34578888888764
No 83
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=29.46 E-value=51 Score=18.28 Aligned_cols=17 Identities=41% Similarity=0.390 Sum_probs=11.6
Q ss_pred CCHHHHHHHHHHcCCCC
Q psy13127 45 VVGAERKQLAQSLSLTE 61 (64)
Q Consensus 45 ~~~~~r~~La~~l~l~~ 61 (64)
.+...|.+||..||++.
T Consensus 83 SSl~aRkeLA~eL~~~~ 99 (127)
T PF12200_consen 83 SSLAARKELAKELGYTG 99 (127)
T ss_dssp -SHHHHHHHHHHHT---
T ss_pred CCHHHHHHHHHHhCCCC
Confidence 46778999999999864
No 84
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=29.33 E-value=62 Score=18.02 Aligned_cols=14 Identities=29% Similarity=0.501 Sum_probs=9.5
Q ss_pred HHHHHHHHcCCCCc
Q psy13127 49 ERKQLAQSLSLTET 62 (64)
Q Consensus 49 ~r~~La~~l~l~~~ 62 (64)
.-.++|..||+++.
T Consensus 145 s~~EIA~~lgis~~ 158 (178)
T PRK12529 145 KQKDIAQALDIALP 158 (178)
T ss_pred CHHHHHHHHCCCHH
Confidence 34577788887764
No 85
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=29.21 E-value=98 Score=16.40 Aligned_cols=36 Identities=8% Similarity=0.056 Sum_probs=20.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 24 RTAFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 24 Rt~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
|..||..+....-.....+-+ ...++|..+|++..+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~t 45 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQ 45 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHH
Confidence 445777765544333222222 345778888887643
No 86
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=29.15 E-value=96 Score=16.40 Aligned_cols=15 Identities=13% Similarity=0.330 Sum_probs=9.5
Q ss_pred HHHHHHHcCCCCcCC
Q psy13127 50 RKQLAQSLSLTETQF 64 (64)
Q Consensus 50 r~~La~~l~l~~~qV 64 (64)
-.++|..||++...|
T Consensus 126 ~~EIA~~l~is~~tV 140 (142)
T TIGR03209 126 EIDIAKKLHISRQSV 140 (142)
T ss_pred HHHHHHHHCcCHHhh
Confidence 346777777776543
No 87
>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=29.04 E-value=6.7 Score=18.52 Aligned_cols=15 Identities=20% Similarity=0.401 Sum_probs=11.1
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
...++|..||++...
T Consensus 15 ~~~eIA~~Lg~~~~T 29 (58)
T PF06056_consen 15 SIKEIAEELGVPRST 29 (58)
T ss_pred CHHHHHHHHCCChHH
Confidence 456789999988654
No 88
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.19 E-value=64 Score=18.04 Aligned_cols=14 Identities=14% Similarity=0.178 Sum_probs=9.9
Q ss_pred HHHHHHHHcCCCCc
Q psy13127 49 ERKQLAQSLSLTET 62 (64)
Q Consensus 49 ~r~~La~~l~l~~~ 62 (64)
.-.++|..+|++..
T Consensus 157 s~~EIA~~lgis~~ 170 (189)
T PRK09648 157 SAEETAEAVGSTPG 170 (189)
T ss_pred CHHHHHHHHCCCHH
Confidence 45577888888764
No 89
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=27.06 E-value=89 Score=17.63 Aligned_cols=15 Identities=13% Similarity=0.253 Sum_probs=9.3
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..||++...
T Consensus 160 s~~EIA~~Lgis~~t 174 (194)
T PRK09646 160 TYREVAERLAVPLGT 174 (194)
T ss_pred CHHHHHHHhCCChHh
Confidence 345677777776643
No 90
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=26.92 E-value=74 Score=17.20 Aligned_cols=15 Identities=27% Similarity=0.457 Sum_probs=9.8
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
...++|..+|++...
T Consensus 127 s~~EIA~~lgis~~t 141 (163)
T PRK07037 127 TQKDIARELGVSPTL 141 (163)
T ss_pred CHHHHHHHHCCCHHH
Confidence 345777778777643
No 91
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=26.70 E-value=75 Score=17.05 Aligned_cols=14 Identities=14% Similarity=0.173 Sum_probs=9.6
Q ss_pred HHHHHHHcCCCCcC
Q psy13127 50 RKQLAQSLSLTETQ 63 (64)
Q Consensus 50 r~~La~~l~l~~~q 63 (64)
-.++|..||++...
T Consensus 125 ~~EIA~~lgis~~t 138 (161)
T PRK09047 125 VAETAAAMGCSEGS 138 (161)
T ss_pred HHHHHHHHCCCHHH
Confidence 45778888887643
No 92
>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=26.20 E-value=52 Score=14.15 Aligned_cols=29 Identities=28% Similarity=0.332 Sum_probs=15.9
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 30 SQLLKLEHAFEKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 30 ~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
.+...|....+ ++.. ...+||..+|++..
T Consensus 4 ~~~~Il~~l~~-~~~~---t~~ela~~~~is~~ 32 (48)
T PF13412_consen 4 TQRKILNYLRE-NPRI---TQKELAEKLGISRS 32 (48)
T ss_dssp HHHHHHHHHHH-CTTS----HHHHHHHHTS-HH
T ss_pred HHHHHHHHHHH-cCCC---CHHHHHHHhCCCHH
Confidence 44445543333 4433 45688999998754
No 93
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.14 E-value=79 Score=17.06 Aligned_cols=14 Identities=7% Similarity=0.083 Sum_probs=8.6
Q ss_pred HHHHHHHcCCCCcC
Q psy13127 50 RKQLAQSLSLTETQ 63 (64)
Q Consensus 50 r~~La~~l~l~~~q 63 (64)
-.++|..+|++...
T Consensus 125 ~~EIA~~lgis~~t 138 (160)
T PRK09642 125 YQEIALQEKIEVKT 138 (160)
T ss_pred HHHHHHHHCCCHHH
Confidence 34667777776543
No 94
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=25.77 E-value=1.1e+02 Score=17.05 Aligned_cols=15 Identities=20% Similarity=0.206 Sum_probs=9.9
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 151 s~~eIA~~lgis~~t 165 (182)
T PRK12537 151 SHAEIAQRLGAPLGT 165 (182)
T ss_pred CHHHHHHHHCCChhh
Confidence 345677778877654
No 95
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=25.54 E-value=63 Score=17.50 Aligned_cols=13 Identities=23% Similarity=0.284 Sum_probs=7.8
Q ss_pred HHHHHHHcCCCCc
Q psy13127 50 RKQLAQSLSLTET 62 (64)
Q Consensus 50 r~~La~~l~l~~~ 62 (64)
-.++|..+|++..
T Consensus 131 ~~eIA~~lgis~~ 143 (161)
T PRK12541 131 YKEIAEMTGLSLA 143 (161)
T ss_pred HHHHHHHHCCCHH
Confidence 3456666666654
No 96
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=25.24 E-value=80 Score=18.11 Aligned_cols=15 Identities=33% Similarity=0.397 Sum_probs=9.7
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 171 s~~EIA~~lgis~~t 185 (206)
T PRK12526 171 SQEQLAQQLNVPLGT 185 (206)
T ss_pred CHHHHHHHHCCCHHH
Confidence 445677777777643
No 97
>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=24.94 E-value=79 Score=16.23 Aligned_cols=15 Identities=20% Similarity=0.315 Sum_probs=10.3
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 128 s~~eIA~~l~~s~~~ 142 (158)
T TIGR02937 128 SYKEIAEILGISVGT 142 (158)
T ss_pred CHHHHHHHHCCCHHH
Confidence 445788888887643
No 98
>PF13309 HTH_22: HTH domain
Probab=24.92 E-value=93 Score=14.71 Aligned_cols=37 Identities=14% Similarity=0.297 Sum_probs=21.9
Q ss_pred CCHHHHH-HHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 27 FSPSQLL-KLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 27 ~t~~q~~-~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
.+..+.. ......+..-|.-...-..+|..||++...
T Consensus 21 l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~T 58 (64)
T PF13309_consen 21 LSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRAT 58 (64)
T ss_pred CCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHH
Confidence 3444444 344445555555555666899999988643
No 99
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=24.91 E-value=86 Score=17.38 Aligned_cols=15 Identities=33% Similarity=0.368 Sum_probs=9.6
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 149 s~~eIA~~l~is~~t 163 (184)
T PRK12512 149 SIKETAAKLSMSEGA 163 (184)
T ss_pred CHHHHHHHhCCCHHH
Confidence 345677777777643
No 100
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, 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, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=24.87 E-value=26 Score=17.75 Aligned_cols=13 Identities=31% Similarity=0.473 Sum_probs=10.3
Q ss_pred HHHHHHcCCCCcC
Q psy13127 51 KQLAQSLSLTETQ 63 (64)
Q Consensus 51 ~~La~~l~l~~~q 63 (64)
..||..||+++..
T Consensus 17 ~~Lar~Lgls~~~ 29 (83)
T cd08319 17 EQVLLDLGLSQTD 29 (83)
T ss_pred HHHHHHcCCCHHH
Confidence 4689999998754
No 101
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=24.76 E-value=97 Score=16.94 Aligned_cols=13 Identities=31% Similarity=0.447 Sum_probs=8.9
Q ss_pred HHHHHHHcCCCCc
Q psy13127 50 RKQLAQSLSLTET 62 (64)
Q Consensus 50 r~~La~~l~l~~~ 62 (64)
-.++|..||+++.
T Consensus 137 ~~EIA~~lgis~~ 149 (173)
T PRK09645 137 TAQIAADLGIPEG 149 (173)
T ss_pred HHHHHHHHCcCHH
Confidence 4567777777764
No 102
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=24.47 E-value=84 Score=17.34 Aligned_cols=15 Identities=13% Similarity=0.251 Sum_probs=9.4
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 152 s~~EIA~~lgis~~t 166 (183)
T TIGR02999 152 TVEEIAELLGVSVRT 166 (183)
T ss_pred CHHHHHHHhCCCHHH
Confidence 345677777777643
No 103
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=24.46 E-value=17 Score=19.00 Aligned_cols=16 Identities=31% Similarity=0.507 Sum_probs=10.4
Q ss_pred HHHHHHHHcCCCCcCC
Q psy13127 49 ERKQLAQSLSLTETQF 64 (64)
Q Consensus 49 ~r~~La~~l~l~~~qV 64 (64)
...+||.+.|||+.+|
T Consensus 74 n~~eLA~kyglS~r~I 89 (108)
T PF08765_consen 74 NVRELARKYGLSERQI 89 (108)
T ss_dssp -HHHHHHHHT--HHHH
T ss_pred CHHHHHHHHCcCHHHH
Confidence 4568999999998654
No 104
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=24.27 E-value=78 Score=17.19 Aligned_cols=14 Identities=7% Similarity=0.102 Sum_probs=9.4
Q ss_pred HHHHHHHcCCCCcC
Q psy13127 50 RKQLAQSLSLTETQ 63 (64)
Q Consensus 50 r~~La~~l~l~~~q 63 (64)
-.++|..+|++...
T Consensus 147 ~~eIA~~lgis~~t 160 (182)
T PRK09652 147 YEEIAEIMGCPIGT 160 (182)
T ss_pred HHHHHHHHCCCHHH
Confidence 44677778877643
No 105
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=24.24 E-value=78 Score=18.45 Aligned_cols=15 Identities=20% Similarity=0.441 Sum_probs=11.1
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
...++|..+|++...
T Consensus 201 t~~eIA~~lgis~~~ 215 (231)
T TIGR02885 201 TQTEVANMLGISQVQ 215 (231)
T ss_pred CHHHHHHHHCcCHHH
Confidence 456788888888654
No 106
>PF14174 YycC: YycC-like protein
Probab=24.03 E-value=46 Score=15.48 Aligned_cols=18 Identities=17% Similarity=0.174 Sum_probs=12.3
Q ss_pred CHHHHHHHHHHcCCCCcC
Q psy13127 46 VGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 46 ~~~~r~~La~~l~l~~~q 63 (64)
+..+-..||..||++-.+
T Consensus 7 S~eTA~kLs~~L~vPlE~ 24 (53)
T PF14174_consen 7 SPETAVKLSKKLGVPLEQ 24 (53)
T ss_pred CHHHHHHHHHHHCCcHHH
Confidence 445566788888887543
No 107
>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=24.02 E-value=88 Score=16.54 Aligned_cols=15 Identities=20% Similarity=0.386 Sum_probs=10.0
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
...++|..+|+++..
T Consensus 131 ~~~eIA~~lgis~~t 145 (161)
T TIGR02985 131 SYKEIAEELGISVKT 145 (161)
T ss_pred CHHHHHHHHCCCHHH
Confidence 445677888887653
No 108
>PRK15372 pathogenicity island 2 effector protein SseI; Provisional
Probab=23.85 E-value=66 Score=20.12 Aligned_cols=31 Identities=23% Similarity=0.209 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Q psy13127 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQS 56 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~ 56 (64)
-++..|-.+|+..|...+.|....+++++..
T Consensus 11 FcsTHq~EAl~CI~~LcHP~~gtTpe~I~s~ 41 (292)
T PRK15372 11 FCSTHQTEALECIWTICHPPAGTTREDVVSR 41 (292)
T ss_pred hccccHHHHHHHHHHHhCCCCCCCHHHHHHH
Confidence 3577888999999999998877666666544
No 109
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=23.67 E-value=86 Score=16.96 Aligned_cols=14 Identities=29% Similarity=0.230 Sum_probs=8.5
Q ss_pred HHHHHHHHcCCCCc
Q psy13127 49 ERKQLAQSLSLTET 62 (64)
Q Consensus 49 ~r~~La~~l~l~~~ 62 (64)
.-.++|..||++..
T Consensus 140 s~~eIA~~l~is~~ 153 (170)
T TIGR02952 140 PIAEVARILGKTEG 153 (170)
T ss_pred CHHHHHHHHCCCHH
Confidence 34466777777654
No 110
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=23.66 E-value=99 Score=16.86 Aligned_cols=15 Identities=20% Similarity=0.279 Sum_probs=10.1
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 137 s~~eiA~~lgis~~t 151 (169)
T TIGR02954 137 TIKEIAEVMNKPEGT 151 (169)
T ss_pred CHHHHHHHHCCCHHH
Confidence 345778888887654
No 111
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=23.56 E-value=1e+02 Score=17.71 Aligned_cols=38 Identities=21% Similarity=0.286 Sum_probs=24.6
Q ss_pred CCCCCCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHcCC
Q psy13127 22 RIRTAFSPSQLLKLEHAFEK-----NHYVVGAERKQLAQSLSL 59 (64)
Q Consensus 22 r~Rt~~t~~q~~~Le~~F~~-----~~~~~~~~r~~La~~l~l 59 (64)
...+.|+..|++.|...|.. +-+.+..+-..+-..+|.
T Consensus 9 ~~~~~~t~~qi~~lkeaF~l~D~d~~G~I~~~el~~ilr~lg~ 51 (160)
T COG5126 9 LTFTQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGF 51 (160)
T ss_pred hhcccCCHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHcCC
Confidence 35788999999999999884 224444444444334443
No 112
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=23.36 E-value=93 Score=17.39 Aligned_cols=13 Identities=8% Similarity=0.343 Sum_probs=8.3
Q ss_pred HHHHHHHcCCCCc
Q psy13127 50 RKQLAQSLSLTET 62 (64)
Q Consensus 50 r~~La~~l~l~~~ 62 (64)
-.++|..+|++..
T Consensus 150 ~~eIA~~lgis~~ 162 (189)
T PRK12515 150 VEEVGEIVGIPES 162 (189)
T ss_pred HHHHHHHHCcCHH
Confidence 4466777777654
No 113
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, 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=23.34 E-value=29 Score=17.47 Aligned_cols=31 Identities=16% Similarity=0.325 Sum_probs=19.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
+.|..|+..+-...-. .=..||..||+++..
T Consensus 4 ~~t~~~l~~ia~~iG~-------~Wk~Lar~LGls~~d 34 (86)
T cd08318 4 PVTGEQITVFANKLGE-------DWKTLAPHLEMKDKE 34 (86)
T ss_pred CCCHHHHHHHHHHHhh-------hHHHHHHHcCCCHHH
Confidence 4567777776532221 224699999998754
No 114
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=22.96 E-value=1.2e+02 Score=20.15 Aligned_cols=25 Identities=20% Similarity=0.318 Sum_probs=19.9
Q ss_pred hhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 40 EKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 40 ~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
+..-|++......+|..|||+..+|
T Consensus 48 e~~GyIp~~ai~~VAe~Lgvp~~~V 72 (400)
T PRK12373 48 EQEGWVTRAAIEKVADMLDMAYIRV 72 (400)
T ss_pred HHcCCCCHHHHHHHHHHhCCCHHHH
Confidence 3445889999999999999987654
No 115
>PF06918 DUF1280: Protein of unknown function (DUF1280); InterPro: IPR009689 This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to Caenorhabditis elegans.
Probab=22.78 E-value=1.9e+02 Score=17.48 Aligned_cols=39 Identities=13% Similarity=0.227 Sum_probs=31.9
Q ss_pred CCCCCCHHHHHHHHHHHhh----cCCCCHHHHHHHHHHcCCCC
Q psy13127 23 IRTAFSPSQLLKLEHAFEK----NHYVVGAERKQLAQSLSLTE 61 (64)
Q Consensus 23 ~Rt~~t~~q~~~Le~~F~~----~~~~~~~~r~~La~~l~l~~ 61 (64)
.+..+|..++..+.+.|.. +.+|+.....+|...++..+
T Consensus 61 ~k~~LSd~~lk~~K~~~k~~lg~Dvf~Sr~~i~~l~k~~s~~~ 103 (224)
T PF06918_consen 61 VKFNLSDGFLKKFKKFLKEFLGFDVFPSRKSIDELEKKVSSID 103 (224)
T ss_pred EEecCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHhcCccc
Confidence 3677899999999999887 67899999888888876543
No 116
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.73 E-value=1.2e+02 Score=16.64 Aligned_cols=15 Identities=20% Similarity=0.211 Sum_probs=10.4
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 147 s~~eIA~~lgis~~t 161 (179)
T PRK12514 147 SYKELAERHDVPLNT 161 (179)
T ss_pred CHHHHHHHHCCChHH
Confidence 355778888887654
No 117
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=22.62 E-value=1.4e+02 Score=16.62 Aligned_cols=15 Identities=13% Similarity=0.029 Sum_probs=10.2
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 155 s~~eIA~~lgis~~~ 169 (187)
T PRK12534 155 TYEELAARTDTPIGT 169 (187)
T ss_pred CHHHHHHHhCCChhH
Confidence 345778888887654
No 118
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=22.55 E-value=29 Score=19.78 Aligned_cols=22 Identities=23% Similarity=0.238 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHHHHcCCCCcCC
Q psy13127 43 HYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 43 ~~~~~~~r~~La~~l~l~~~qV 64 (64)
.++..-...++|..||+++..|
T Consensus 45 ~~l~PLt~~~iA~~lgl~~STV 66 (160)
T PF04552_consen 45 GALKPLTMKDIADELGLHESTV 66 (160)
T ss_dssp ----------------------
T ss_pred ccCcCCCHHHHHHHhCCCHhHH
Confidence 3555567778999999998754
No 119
>KOG1691|consensus
Probab=22.51 E-value=94 Score=18.74 Aligned_cols=17 Identities=29% Similarity=0.381 Sum_probs=13.7
Q ss_pred CHHHHHHHHHHHhhcCC
Q psy13127 28 SPSQLLKLEHAFEKNHY 44 (64)
Q Consensus 28 t~~q~~~Le~~F~~~~~ 44 (64)
..+|+..|.+.|++++.
T Consensus 193 a~~QvlyLK~fF~kKKL 209 (210)
T KOG1691|consen 193 AGWQVLYLKRFFQKKKL 209 (210)
T ss_pred HHHHHHHHHHHHHhccC
Confidence 46899999999988753
No 120
>PRK00118 putative DNA-binding protein; Validated
Probab=22.51 E-value=1.1e+02 Score=16.26 Aligned_cols=31 Identities=10% Similarity=0.173 Sum_probs=18.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCc
Q psy13127 27 FSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTET 62 (64)
Q Consensus 27 ~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~ 62 (64)
.+..|...+...|..+. .-.++|..+|++..
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~ 48 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQ 48 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHH
Confidence 34555565554444332 45578888888764
No 121
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=22.07 E-value=84 Score=14.01 Aligned_cols=13 Identities=31% Similarity=0.626 Sum_probs=9.1
Q ss_pred HHHHHHcCCCCcC
Q psy13127 51 KQLAQSLSLTETQ 63 (64)
Q Consensus 51 ~~La~~l~l~~~q 63 (64)
..||..+|+++.+
T Consensus 46 ~~la~~~~i~~~~ 58 (59)
T PF10410_consen 46 RELAERLGISEDA 58 (59)
T ss_dssp HHHHHHCT-SSTT
T ss_pred HHHHHHhCcCccc
Confidence 4688888888765
No 122
>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=22.03 E-value=96 Score=16.71 Aligned_cols=15 Identities=20% Similarity=0.348 Sum_probs=10.2
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 128 s~~eIA~~lgis~~t 142 (162)
T TIGR02983 128 SEAQVAEALGISVGT 142 (162)
T ss_pred CHHHHHHHhCCCHHH
Confidence 345778888887654
No 123
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=22.01 E-value=64 Score=17.26 Aligned_cols=31 Identities=16% Similarity=0.141 Sum_probs=18.8
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 31 QLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 31 q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
+...|...|....+ .....+||..+.++++.
T Consensus 5 ~y~~L~~~~~~~~~--~vtl~elA~~l~cS~Rn 35 (115)
T PF12793_consen 5 QYQRLWQHYGGQPV--EVTLDELAELLFCSRRN 35 (115)
T ss_pred HHHHHHHHcCCCCc--ceeHHHHHHHhCCCHHH
Confidence 34455555553332 23456899999998764
No 124
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, 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
Probab=21.92 E-value=34 Score=17.26 Aligned_cols=13 Identities=15% Similarity=0.296 Sum_probs=10.3
Q ss_pred HHHHHHcCCCCcC
Q psy13127 51 KQLAQSLSLTETQ 63 (64)
Q Consensus 51 ~~La~~l~l~~~q 63 (64)
..||..||+++..
T Consensus 17 k~lar~LGlse~~ 29 (86)
T cd08779 17 QAIGLHLGLSYRE 29 (86)
T ss_pred HHHHHHcCCCHHH
Confidence 4789999998754
No 125
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=21.77 E-value=1e+02 Score=16.61 Aligned_cols=15 Identities=13% Similarity=0.251 Sum_probs=10.4
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|++...
T Consensus 143 ~~~eIA~~lgis~~t 157 (179)
T PRK11924 143 SYREIAEILGVPVGT 157 (179)
T ss_pred CHHHHHHHHCCCHHH
Confidence 345788888887654
No 126
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.53 E-value=98 Score=17.43 Aligned_cols=15 Identities=13% Similarity=0.346 Sum_probs=10.4
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.-.++|..+|+++..
T Consensus 152 s~~EIA~~lgis~~t 166 (189)
T PRK12530 152 SSEQICQECDISTSN 166 (189)
T ss_pred CHHHHHHHHCCCHHH
Confidence 345788888887653
No 127
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=21.43 E-value=93 Score=18.59 Aligned_cols=33 Identities=15% Similarity=0.309 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcC
Q psy13127 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQ 63 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~q 63 (64)
.++..+...+...|..+ ....++|..+|++...
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~ 241 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQ 241 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHH
Confidence 34555555555555322 2456889999988754
No 128
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.31 E-value=99 Score=16.70 Aligned_cols=13 Identities=31% Similarity=0.603 Sum_probs=7.7
Q ss_pred HHHHHHHcCCCCc
Q psy13127 50 RKQLAQSLSLTET 62 (64)
Q Consensus 50 r~~La~~l~l~~~ 62 (64)
-.++|..+|++..
T Consensus 130 ~~eIA~~lgis~~ 142 (166)
T PRK09639 130 YKEIAEALGIKES 142 (166)
T ss_pred HHHHHHHHCCCHH
Confidence 4456666666654
No 129
>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=21.21 E-value=98 Score=15.98 Aligned_cols=15 Identities=27% Similarity=0.481 Sum_probs=11.0
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.=..||..|||++..
T Consensus 21 ~Wk~laR~LGLse~~ 35 (96)
T cd08315 21 SWNRLMRQLGLSENE 35 (96)
T ss_pred HHHHHHHHcCCCHHH
Confidence 345789999998754
No 130
>PF13518 HTH_28: Helix-turn-helix domain
Probab=21.09 E-value=38 Score=14.64 Aligned_cols=16 Identities=6% Similarity=0.380 Sum_probs=11.0
Q ss_pred HHHHHHHHcCCCCcCC
Q psy13127 49 ERKQLAQSLSLTETQF 64 (64)
Q Consensus 49 ~r~~La~~l~l~~~qV 64 (64)
...++|..+|++..+|
T Consensus 14 s~~~~a~~~gis~~tv 29 (52)
T PF13518_consen 14 SVREIAREFGISRSTV 29 (52)
T ss_pred CHHHHHHHHCCCHhHH
Confidence 3456888888876543
No 131
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=20.96 E-value=55 Score=17.00 Aligned_cols=16 Identities=19% Similarity=0.491 Sum_probs=12.8
Q ss_pred HHHHHHHHcCCCCcCC
Q psy13127 49 ERKQLAQSLSLTETQF 64 (64)
Q Consensus 49 ~r~~La~~l~l~~~qV 64 (64)
....+|..+|+.+.+|
T Consensus 25 gq~~vA~~~Gv~eStI 40 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTI 40 (91)
T ss_dssp HHHHHHHHHTSSTTTH
T ss_pred hhHHHHHHhCCCHHHH
Confidence 3457899999999875
No 132
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=20.81 E-value=1.1e+02 Score=17.21 Aligned_cols=14 Identities=14% Similarity=0.124 Sum_probs=9.2
Q ss_pred HHHHHHHHcCCCCc
Q psy13127 49 ERKQLAQSLSLTET 62 (64)
Q Consensus 49 ~r~~La~~l~l~~~ 62 (64)
.-.++|..+|++..
T Consensus 129 s~~EIA~~lgis~~ 142 (182)
T PRK12511 129 SYQEAAAVLGIPIG 142 (182)
T ss_pred CHHHHHHHhCcCHH
Confidence 34567777777764
No 133
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.79 E-value=1.1e+02 Score=16.71 Aligned_cols=14 Identities=7% Similarity=-0.123 Sum_probs=9.2
Q ss_pred HHHHHHHHcCCCCc
Q psy13127 49 ERKQLAQSLSLTET 62 (64)
Q Consensus 49 ~r~~La~~l~l~~~ 62 (64)
.-.++|..+|++..
T Consensus 130 s~~eIA~~lgis~~ 143 (164)
T PRK12547 130 SYEDAAAICGCAVG 143 (164)
T ss_pred CHHHHHHHhCCCHH
Confidence 34567777777764
No 134
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=20.66 E-value=1.2e+02 Score=19.82 Aligned_cols=32 Identities=19% Similarity=0.146 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 30 SQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 30 ~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+...|...+..+.+.+.. .||..++++.++|
T Consensus 5 ~~~~~l~~l~~~~~~~~~~---~la~~l~vS~Rti 36 (491)
T COG3711 5 RREQLLLLLLLKNPLLTIK---ELAEQLGVSRRTI 36 (491)
T ss_pred HHHHHHHHHHHhCCCCCHH---HHHHHhCccHHHH
Confidence 3445566667788887665 6788999988754
No 135
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. 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=20.22 E-value=39 Score=16.69 Aligned_cols=15 Identities=20% Similarity=0.514 Sum_probs=11.2
Q ss_pred HHHHHHHHcCCCCcC
Q psy13127 49 ERKQLAQSLSLTETQ 63 (64)
Q Consensus 49 ~r~~La~~l~l~~~q 63 (64)
.=..||..||+++..
T Consensus 13 ~Wk~laR~LGls~~~ 27 (79)
T cd08784 13 QHKRFFRKLGLSDNE 27 (79)
T ss_pred HHHHHHHHcCCCHHH
Confidence 335799999998754
No 136
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=20.01 E-value=1.1e+02 Score=17.79 Aligned_cols=38 Identities=13% Similarity=0.223 Sum_probs=23.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCCcCC
Q psy13127 26 AFSPSQLLKLEHAFEKNHYVVGAERKQLAQSLSLTETQF 64 (64)
Q Consensus 26 ~~t~~q~~~Le~~F~~~~~~~~~~r~~La~~l~l~~~qV 64 (64)
.+|..++..+......+ +-....-.++|..+++++..|
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv 195 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSC 195 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHH
Confidence 36777666665544432 333345568999999987643
Done!