Query psy7107
Match_columns 76
No_of_seqs 118 out of 1108
Neff 8.6
Searched_HMMs 46136
Date Fri Aug 16 18:20:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7107.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7107hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0488|consensus 99.5 9.4E-14 2E-18 91.2 5.8 54 22-75 164-217 (309)
2 KOG0484|consensus 99.4 5E-14 1.1E-18 79.4 2.5 53 23-75 10-62 (125)
3 TIGR01565 homeo_ZF_HD homeobox 99.4 1.8E-12 3.9E-17 66.5 5.4 45 31-75 2-50 (58)
4 KOG2251|consensus 99.4 9.7E-13 2.1E-17 82.3 4.6 52 25-76 32-83 (228)
5 KOG0842|consensus 99.3 2.2E-12 4.9E-17 84.4 5.8 50 26-75 149-198 (307)
6 KOG0850|consensus 99.3 1.3E-12 2.9E-17 82.2 4.2 50 26-75 118-167 (245)
7 KOG0843|consensus 99.3 3.5E-12 7.5E-17 77.9 4.3 47 29-75 101-147 (197)
8 KOG0489|consensus 99.3 2.9E-12 6.3E-17 82.6 3.5 48 28-75 157-204 (261)
9 KOG0493|consensus 99.3 1E-11 2.2E-16 79.8 5.3 45 31-75 247-291 (342)
10 KOG0487|consensus 99.2 2.7E-11 5.8E-16 79.4 4.9 51 25-75 230-280 (308)
11 PF00046 Homeobox: Homeobox do 99.2 2.9E-11 6.2E-16 61.3 3.7 46 31-76 1-46 (57)
12 KOG0485|consensus 99.2 4.3E-11 9.3E-16 75.2 4.4 50 26-75 100-149 (268)
13 KOG0494|consensus 99.1 4.3E-10 9.4E-15 72.3 5.5 47 29-75 140-186 (332)
14 KOG0486|consensus 99.0 3E-10 6.4E-15 74.4 4.0 48 28-75 110-157 (351)
15 smart00389 HOX Homeodomain. DN 99.0 8.1E-10 1.8E-14 55.6 4.7 45 32-76 2-46 (56)
16 KOG0492|consensus 99.0 4.4E-10 9.6E-15 70.2 4.3 47 29-75 143-189 (246)
17 cd00086 homeodomain Homeodomai 98.9 2.3E-09 5E-14 54.2 4.6 45 32-76 2-46 (59)
18 KOG0844|consensus 98.9 6.3E-10 1.4E-14 73.0 2.9 51 25-75 176-226 (408)
19 KOG0848|consensus 98.9 4.6E-10 9.9E-15 72.3 1.5 49 27-75 196-244 (317)
20 KOG0491|consensus 98.8 5.6E-10 1.2E-14 67.6 0.3 46 30-75 100-145 (194)
21 KOG0490|consensus 98.6 3.3E-08 7.2E-13 61.8 2.8 50 27-76 57-106 (235)
22 KOG0849|consensus 98.6 1E-07 2.3E-12 63.9 4.7 53 23-75 169-221 (354)
23 COG5576 Homeodomain-containing 98.4 6.6E-07 1.4E-11 54.1 5.0 48 28-75 49-96 (156)
24 KOG3802|consensus 98.0 1E-05 2.3E-10 54.8 4.6 47 29-75 293-339 (398)
25 KOG0847|consensus 98.0 5E-06 1.1E-10 52.8 2.4 50 26-75 163-212 (288)
26 KOG0483|consensus 97.9 1.9E-05 4.2E-10 49.4 3.8 45 31-75 51-95 (198)
27 KOG2252|consensus 97.7 6.3E-05 1.4E-09 52.8 4.6 51 26-76 416-466 (558)
28 KOG4577|consensus 97.5 0.00012 2.5E-09 48.3 3.6 47 29-75 166-212 (383)
29 PF05920 Homeobox_KN: Homeobox 96.7 0.00065 1.4E-08 32.2 0.9 26 51-76 7-32 (40)
30 KOG0774|consensus 96.3 0.0072 1.6E-07 39.6 3.8 46 31-76 189-237 (334)
31 KOG0490|consensus 95.7 0.018 3.9E-07 35.9 3.7 50 26-75 149-198 (235)
32 KOG0775|consensus 95.7 0.02 4.3E-07 37.7 3.9 40 37-76 183-222 (304)
33 KOG1168|consensus 94.7 0.022 4.7E-07 37.9 1.8 47 29-75 308-354 (385)
34 PF04967 HTH_10: HTH DNA bindi 92.7 0.22 4.8E-06 24.9 3.0 38 37-74 1-40 (53)
35 PF04218 CENP-B_N: CENP-B N-te 92.5 0.45 9.7E-06 23.6 4.0 40 31-75 1-40 (53)
36 PF11569 Homez: Homeodomain le 88.6 0.31 6.8E-06 24.7 1.4 35 42-76 10-44 (56)
37 COG3413 Predicted DNA binding 85.0 1.3 2.8E-05 27.7 3.0 38 36-73 155-194 (215)
38 KOG1146|consensus 82.3 3.1 6.7E-05 33.1 4.5 46 30-75 903-948 (1406)
39 PF13936 HTH_38: Helix-turn-he 76.9 3 6.5E-05 19.6 2.1 35 35-74 3-37 (44)
40 PF08280 HTH_Mga: M protein tr 73.2 3.9 8.4E-05 20.4 2.0 32 41-76 7-38 (59)
41 PF04545 Sigma70_r4: Sigma-70, 70.9 7.2 0.00016 18.4 2.7 34 37-75 5-38 (50)
42 PF12824 MRP-L20: Mitochondria 70.5 13 0.00029 22.7 4.3 38 33-72 82-119 (164)
43 PF01527 HTH_Tnp_1: Transposas 69.2 7.3 0.00016 19.9 2.6 38 32-74 2-40 (76)
44 COG4367 Uncharacterized protei 68.8 7 0.00015 21.7 2.5 38 37-74 3-40 (97)
45 PF09607 BrkDBD: Brinker DNA-b 60.4 16 0.00035 18.6 2.7 41 34-75 3-43 (58)
46 PF08880 QLQ: QLQ; InterPro: 59.6 11 0.00024 17.3 1.9 14 36-49 2-15 (37)
47 PF06971 Put_DNA-bind_N: Putat 56.5 4.1 8.8E-05 20.0 0.2 16 61-76 32-47 (50)
48 PRK13558 bacterio-opsin activa 54.4 17 0.00037 26.2 3.1 40 35-74 606-647 (665)
49 KOG0773|consensus 54.2 26 0.00055 23.4 3.7 46 31-76 240-288 (342)
50 PF02796 HTH_7: Helix-turn-hel 52.6 25 0.00053 16.4 2.7 33 37-74 6-38 (45)
51 PF08279 HTH_11: HTH domain; 51.6 18 0.00039 17.2 2.1 17 59-75 17-33 (55)
52 TIGR03879 near_KaiC_dom probab 50.5 3 6.5E-05 22.2 -0.9 30 46-75 21-50 (73)
53 TIGR01958 nuoE_fam NADH-quinon 47.9 47 0.001 19.6 3.8 25 50-74 27-51 (148)
54 PRK07539 NADH dehydrogenase su 47.0 48 0.001 19.7 3.8 25 50-74 33-57 (154)
55 PF10668 Phage_terminase: Phag 46.9 10 0.00022 19.4 0.8 16 60-75 25-40 (60)
56 PRK05988 formate dehydrogenase 46.4 52 0.0011 19.8 3.9 32 43-74 27-58 (156)
57 PF13404 HTH_AsnC-type: AsnC-t 45.1 12 0.00025 17.5 0.8 16 60-75 20-35 (42)
58 PRK03975 tfx putative transcri 43.8 33 0.00072 20.5 2.7 35 35-75 5-39 (141)
59 PF08281 Sigma70_r4_2: Sigma-7 42.6 6.6 0.00014 18.8 -0.3 23 53-75 22-44 (54)
60 PF01257 2Fe-2S_thioredx: Thio 42.4 44 0.00095 19.7 3.1 33 43-75 17-49 (145)
61 PF05848 CtsR: Firmicute trans 40.7 21 0.00045 21.7 1.5 16 59-74 27-42 (152)
62 PF00196 GerE: Bacterial regul 40.5 43 0.00094 16.2 2.5 34 36-75 3-36 (58)
63 PRK07571 bidirectional hydroge 39.7 74 0.0016 19.5 3.9 25 50-74 47-71 (169)
64 cd08313 Death_TNFR1 Death doma 39.7 34 0.00075 18.3 2.2 18 58-75 12-29 (80)
65 cd08315 Death_TRAILR_DR4_DR5 D 39.6 51 0.0011 18.2 2.9 31 44-74 5-36 (96)
66 cd06171 Sigma70_r4 Sigma70, re 39.5 40 0.00086 15.0 2.5 34 37-75 11-44 (55)
67 PF10078 DUF2316: Uncharacteri 39.4 14 0.00031 20.4 0.6 28 44-75 14-41 (89)
68 TIGR03209 P21_Cbot clostridium 38.7 65 0.0014 18.2 3.4 18 59-76 125-142 (142)
69 COG1905 NuoE NADH:ubiquinone o 38.2 79 0.0017 19.4 3.8 36 39-74 25-60 (160)
70 cd08318 Death_NMPP84 Death dom 37.4 69 0.0015 17.1 3.4 33 36-75 4-36 (86)
71 PRK06759 RNA polymerase factor 34.5 54 0.0012 18.7 2.6 18 58-75 123-140 (154)
72 TIGR02959 SigZ RNA polymerase 34.2 55 0.0012 19.3 2.7 17 59-75 118-134 (170)
73 KOG4565|consensus 33.4 94 0.002 19.5 3.6 23 27-49 109-131 (206)
74 PF08765 Mor: Mor transcriptio 32.7 15 0.00033 20.5 0.1 17 59-75 74-90 (108)
75 PRK09642 RNA polymerase sigma 31.6 65 0.0014 18.6 2.7 17 59-75 124-140 (160)
76 PF06056 Terminase_5: Putative 30.9 8 0.00017 19.5 -1.2 17 59-75 15-31 (58)
77 TIGR00721 tfx DNA-binding prot 30.5 72 0.0016 18.9 2.7 36 34-75 4-39 (137)
78 PF12793 SgrR_N: Sugar transpo 30.3 61 0.0013 18.5 2.3 33 41-75 5-37 (115)
79 PRK15411 rcsA colanic acid cap 30.0 16 0.00035 22.6 -0.2 35 36-76 137-171 (207)
80 PF04539 Sigma70_r3: Sigma-70 29.8 29 0.00063 17.7 0.9 17 59-75 22-38 (78)
81 PRK10430 DNA-binding transcrip 29.4 60 0.0013 20.1 2.4 40 36-76 158-197 (239)
82 PF13730 HTH_36: Helix-turn-he 29.3 36 0.00077 16.1 1.1 18 58-75 26-43 (55)
83 TIGR02989 Sig-70_gvs1 RNA poly 29.2 77 0.0017 18.1 2.7 18 58-75 128-145 (159)
84 PRK04217 hypothetical protein; 29.2 77 0.0017 18.1 2.6 37 34-75 40-76 (110)
85 PRK12529 RNA polymerase sigma 28.8 97 0.0021 18.4 3.1 17 59-75 145-161 (178)
86 PRK09047 RNA polymerase factor 28.8 79 0.0017 18.1 2.7 17 59-75 124-140 (161)
87 TIGR02999 Sig-70_X6 RNA polyme 27.7 82 0.0018 18.5 2.7 17 59-75 152-168 (183)
88 KOG0041|consensus 27.6 1.4E+02 0.0031 19.3 3.8 37 36-72 92-133 (244)
89 PRK09652 RNA polymerase sigma 27.5 76 0.0016 18.4 2.5 17 59-75 146-162 (182)
90 cd08306 Death_FADD Fas-associa 27.4 55 0.0012 17.6 1.7 16 59-74 15-30 (86)
91 cd00569 HTH_Hin_like Helix-tur 26.8 55 0.0012 12.8 3.5 33 37-74 6-38 (42)
92 PRK09646 RNA polymerase sigma 26.3 91 0.002 18.8 2.7 17 59-75 160-176 (194)
93 PRK12515 RNA polymerase sigma 26.2 90 0.0019 18.6 2.7 17 59-75 149-165 (189)
94 PRK07037 extracytoplasmic-func 26.1 1.2E+02 0.0025 17.5 3.1 17 59-75 127-143 (163)
95 TIGR02952 Sig70_famx2 RNA poly 25.4 92 0.002 18.0 2.6 17 59-75 140-156 (170)
96 PF02042 RWP-RK: RWP-RK domain 25.2 84 0.0018 15.5 2.0 14 62-75 20-33 (52)
97 PRK15183 Vi polysaccharide bio 24.5 83 0.0018 18.2 2.1 36 36-71 95-130 (143)
98 PRK12526 RNA polymerase sigma 24.2 1E+02 0.0022 18.9 2.7 18 58-75 170-187 (206)
99 cd08784 Death_DRs Death Domain 24.2 81 0.0018 16.6 2.0 19 57-75 11-29 (79)
100 PRK09645 RNA polymerase sigma 24.0 1.1E+02 0.0023 17.9 2.7 17 59-75 136-152 (173)
101 PRK12537 RNA polymerase sigma 24.0 1.1E+02 0.0024 18.1 2.8 17 59-75 151-167 (182)
102 TIGR02985 Sig70_bacteroi1 RNA 24.0 1.1E+02 0.0023 17.3 2.7 17 59-75 131-147 (161)
103 PF03444 HrcA_DNA-bdg: Winged 23.9 1.1E+02 0.0024 16.4 2.5 31 44-76 12-42 (78)
104 TIGR02954 Sig70_famx3 RNA poly 23.9 1E+02 0.0022 18.0 2.5 17 59-75 137-153 (169)
105 TIGR02983 SigE-fam_strep RNA p 23.8 95 0.0021 17.8 2.4 17 59-75 128-144 (162)
106 PRK09648 RNA polymerase sigma 23.8 1.3E+02 0.0028 17.9 3.1 17 59-75 157-173 (189)
107 cd08319 Death_RAIDD Death doma 23.7 70 0.0015 17.2 1.7 16 59-74 15-30 (83)
108 PRK09639 RNA polymerase sigma 23.4 1E+02 0.0023 17.7 2.6 17 59-75 129-145 (166)
109 PF01726 LexA_DNA_bind: LexA D 23.4 1.2E+02 0.0026 15.4 2.5 32 37-70 4-38 (65)
110 PF07638 Sigma70_ECF: ECF sigm 23.2 1E+02 0.0022 18.6 2.5 18 58-75 152-169 (185)
111 cd08779 Death_PIDD Death Domai 22.7 82 0.0018 16.9 1.8 16 59-74 15-30 (86)
112 PRK12512 RNA polymerase sigma 22.7 1.1E+02 0.0025 18.0 2.7 17 59-75 149-165 (184)
113 PRK12547 RNA polymerase sigma 22.7 1.2E+02 0.0025 17.7 2.7 17 59-75 130-146 (164)
114 PRK12514 RNA polymerase sigma 22.5 1.2E+02 0.0027 17.8 2.8 17 59-75 147-163 (179)
115 cd08316 Death_FAS_TNFRSF6 Deat 21.9 1.1E+02 0.0024 17.0 2.2 17 58-74 21-37 (97)
116 PRK11924 RNA polymerase sigma 21.9 1.1E+02 0.0024 17.6 2.5 17 59-75 143-159 (179)
117 cd01670 Death Death Domain: a 21.9 58 0.0013 16.5 1.1 17 59-75 12-28 (79)
118 PRK12541 RNA polymerase sigma 21.7 1.3E+02 0.0028 17.4 2.7 17 59-75 130-146 (161)
119 cd08777 Death_RIP1 Death Domai 21.5 67 0.0014 17.3 1.3 17 59-75 15-31 (86)
120 PRK09649 RNA polymerase sigma 21.3 1.1E+02 0.0024 18.3 2.4 17 59-75 148-164 (185)
121 PRK12530 RNA polymerase sigma 21.3 1.5E+02 0.0032 17.8 3.0 17 59-75 152-168 (189)
122 PRK13719 conjugal transfer tra 20.9 34 0.00074 22.0 0.1 37 34-76 141-177 (217)
123 PF13384 HTH_23: Homeodomain-l 20.9 36 0.00078 15.7 0.2 17 59-75 19-35 (50)
124 TIGR02937 sigma70-ECF RNA poly 20.8 1.2E+02 0.0027 16.5 2.4 17 59-75 128-144 (158)
125 PRK09643 RNA polymerase sigma 20.6 1.3E+02 0.0028 18.1 2.7 17 59-75 152-168 (192)
126 COG5126 FRQ1 Ca2+-binding prot 20.4 1.2E+02 0.0025 18.6 2.3 39 31-69 8-51 (160)
127 PRK09651 RNA polymerase sigma 20.2 1E+02 0.0022 18.2 2.0 20 56-75 134-153 (172)
128 PRK05602 RNA polymerase sigma 20.1 1.2E+02 0.0026 18.0 2.4 17 59-75 146-162 (186)
129 PRK15372 pathogenicity island 20.0 80 0.0017 21.0 1.6 30 37-66 12-41 (292)
No 1
>KOG0488|consensus
Probab=99.47 E-value=9.4e-14 Score=91.23 Aligned_cols=54 Identities=35% Similarity=0.540 Sum_probs=49.7
Q ss_pred CCCccccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 22 GVLTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 22 ~~~~~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.....++|+|+.||.||..|+.+||+.|++..|++..+|.+||..|||++.|||
T Consensus 164 ~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVK 217 (309)
T KOG0488|consen 164 YQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVK 217 (309)
T ss_pred cccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHH
Confidence 344456888899999999999999999999999999999999999999999997
No 2
>KOG0484|consensus
Probab=99.44 E-value=5e-14 Score=79.37 Aligned_cols=53 Identities=92% Similarity=1.214 Sum_probs=49.1
Q ss_pred CCccccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 23 VLTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 23 ~~~~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
....++|.||.||.||..|+.+||+.|...|||++.+|++||.++.|+++.||
T Consensus 10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQ 62 (125)
T KOG0484|consen 10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQ 62 (125)
T ss_pred ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHH
Confidence 34457788999999999999999999999999999999999999999999886
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=99.37 E-value=1.8e-12 Score=66.46 Aligned_cols=45 Identities=20% Similarity=0.247 Sum_probs=43.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHcCCCcchhc
Q psy7107 31 RRIRTTFTSAQLKELERAFQETHY----PDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 31 rr~Rt~~s~~q~~~Le~~F~~~~y----~~~~~r~~La~~l~l~~~qVk 75 (76)
+|.||.||.+|+..|+..|+.+.| |+...+.+||..|||++.+||
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvK 50 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFK 50 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHee
Confidence 789999999999999999999999 999999999999999999987
No 4
>KOG2251|consensus
Probab=99.36 E-value=9.7e-13 Score=82.33 Aligned_cols=52 Identities=56% Similarity=0.853 Sum_probs=49.5
Q ss_pred ccccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 25 TEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 25 ~~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
...+|.||.||.|+..|+.+||..|.+.+||+...|++||.+|+|++.+||.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV 83 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV 83 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence 5678899999999999999999999999999999999999999999999974
No 5
>KOG0842|consensus
Probab=99.34 E-value=2.2e-12 Score=84.36 Aligned_cols=50 Identities=40% Similarity=0.600 Sum_probs=47.1
Q ss_pred cccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 26 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 26 ~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
..+++||.|..||..|..+||+.|..++|++.++|++||..|.|++.|||
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVK 198 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVK 198 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchhee
Confidence 35677888999999999999999999999999999999999999999998
No 6
>KOG0850|consensus
Probab=99.34 E-value=1.3e-12 Score=82.17 Aligned_cols=50 Identities=38% Similarity=0.611 Sum_probs=47.6
Q ss_pred cccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 26 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 26 ~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
+.+|.|+.||.|+..||..|.+.|++++|+..++|++||..|||+..|||
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVK 167 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVK 167 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhh
Confidence 45778889999999999999999999999999999999999999999997
No 7
>KOG0843|consensus
Probab=99.30 E-value=3.5e-12 Score=77.87 Aligned_cols=47 Identities=38% Similarity=0.605 Sum_probs=45.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 29 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 29 k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
+++|.||.||.+|+..||..|+.++|....+|+.||..|+|++.|||
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVk 147 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVK 147 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhh
Confidence 78899999999999999999999999999999999999999999997
No 8
>KOG0489|consensus
Probab=99.28 E-value=2.9e-12 Score=82.57 Aligned_cols=48 Identities=42% Similarity=0.543 Sum_probs=46.0
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 28 RKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 28 ~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.+.||.||.||..|+.+||..|..|+|++...|.++|..|+|+|+|||
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIK 204 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIK 204 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHH
Confidence 457899999999999999999999999999999999999999999998
No 9
>KOG0493|consensus
Probab=99.26 E-value=1e-11 Score=79.80 Aligned_cols=45 Identities=38% Similarity=0.632 Sum_probs=43.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 31 rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
||.||.||.+||..|...|+.++|+....|.+||..|+|.|.|||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIK 291 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIK 291 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhh
Confidence 578999999999999999999999999999999999999999987
No 10
>KOG0487|consensus
Probab=99.20 E-value=2.7e-11 Score=79.40 Aligned_cols=51 Identities=31% Similarity=0.441 Sum_probs=47.7
Q ss_pred ccccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 25 TEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 25 ~~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
...++.|++|..||..|+.+||++|..|.|++...|.+|++.|+|+++|||
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVK 280 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVK 280 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhee
Confidence 344677889999999999999999999999999999999999999999997
No 11
>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=99.19 E-value=2.9e-11 Score=61.35 Aligned_cols=46 Identities=50% Similarity=0.695 Sum_probs=43.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 31 rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
|+.|+.||.+|+..|+..|..++||+..++..||..+||+..+|++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~ 46 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKN 46 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence 5689999999999999999999999999999999999999999863
No 12
>KOG0485|consensus
Probab=99.16 E-value=4.3e-11 Score=75.16 Aligned_cols=50 Identities=30% Similarity=0.501 Sum_probs=47.0
Q ss_pred cccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 26 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 26 ~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.+.++|+.||+|+..|+..||..|+..+|++..+|..||.+|.|+|.|||
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVK 149 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVK 149 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhh
Confidence 34577889999999999999999999999999999999999999999997
No 13
>KOG0494|consensus
Probab=99.05 E-value=4.3e-10 Score=72.29 Aligned_cols=47 Identities=60% Similarity=0.945 Sum_probs=43.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 29 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 29 k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
++|+.||.||..|+.+||..|...|||+...|+-||.++.|+|.+|+
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIq 186 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQ 186 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhh
Confidence 44455999999999999999999999999999999999999998775
No 14
>KOG0486|consensus
Probab=99.02 E-value=3e-10 Score=74.44 Aligned_cols=48 Identities=65% Similarity=0.871 Sum_probs=45.7
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 28 RKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 28 ~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.|+||.||.|+..|+.+||..|+++.||+..+|+++|.-.+|+|..|.
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvr 157 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 157 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhh
Confidence 378899999999999999999999999999999999999999999885
No 15
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.02 E-value=8.1e-10 Score=55.57 Aligned_cols=45 Identities=49% Similarity=0.739 Sum_probs=42.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 32 RIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 32 r~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
+.|+.|+.+|+..|+..|..++||+..++..||..+||+..+|++
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKV 46 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 467889999999999999999999999999999999999999874
No 16
>KOG0492|consensus
Probab=99.02 E-value=4.4e-10 Score=70.19 Aligned_cols=47 Identities=43% Similarity=0.655 Sum_probs=44.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 29 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 29 k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
-.|+.||.||..|+..||+.|...+|+++.+|.+++..|.|++.|||
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVK 189 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVK 189 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhhee
Confidence 34678999999999999999999999999999999999999999997
No 17
>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=98.94 E-value=2.3e-09 Score=54.23 Aligned_cols=45 Identities=47% Similarity=0.703 Sum_probs=42.3
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 32 RIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 32 r~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
+.+..|+..|+..|+..|..++||+..++..||..+||+..+|++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 467899999999999999999999999999999999999999874
No 18
>KOG0844|consensus
Probab=98.93 E-value=6.3e-10 Score=72.96 Aligned_cols=51 Identities=31% Similarity=0.514 Sum_probs=46.9
Q ss_pred ccccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 25 TEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 25 ~~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
..+...||.||.||.+||..||+.|-+..|.+.+.|-+||..|+|+|..||
T Consensus 176 sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIK 226 (408)
T KOG0844|consen 176 SADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIK 226 (408)
T ss_pred CccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceee
Confidence 345667899999999999999999999999999999999999999998776
No 19
>KOG0848|consensus
Probab=98.91 E-value=4.6e-10 Score=72.34 Aligned_cols=49 Identities=31% Similarity=0.536 Sum_probs=45.2
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 27 KRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 27 ~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.|.+.+.|.+||..|+.+||++|..++|+++..+.+||..|+|+|+|||
T Consensus 196 tRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVK 244 (317)
T KOG0848|consen 196 TRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVK 244 (317)
T ss_pred eecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhh
Confidence 3445577999999999999999999999999999999999999999997
No 20
>KOG0491|consensus
Probab=98.85 E-value=5.6e-10 Score=67.57 Aligned_cols=46 Identities=35% Similarity=0.611 Sum_probs=44.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 30 ~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
+++.||+|+..|+..|+..|+..+|++.+++.+||..|+|++.|||
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVK 145 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVK 145 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHH
Confidence 4678999999999999999999999999999999999999999997
No 21
>KOG0490|consensus
Probab=98.60 E-value=3.3e-08 Score=61.84 Aligned_cols=50 Identities=44% Similarity=0.537 Sum_probs=46.7
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 27 KRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 27 ~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
..+.++.|+.|+.+|+.+|++.|+..|||+...++.||..+++++..||+
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqv 106 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQV 106 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeeh
Confidence 45678999999999999999999999999999999999999999998874
No 22
>KOG0849|consensus
Probab=98.57 E-value=1e-07 Score=63.89 Aligned_cols=53 Identities=47% Similarity=0.662 Sum_probs=47.6
Q ss_pred CCccccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 23 VLTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 23 ~~~~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
....+++.+|.||.|+..|+..|+..|++++||+...|++||.++++++..|+
T Consensus 169 ~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riq 221 (354)
T KOG0849|consen 169 GYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQ 221 (354)
T ss_pred cccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHH
Confidence 33446677888999999999999999999999999999999999999998775
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.42 E-value=6.6e-07 Score=54.06 Aligned_cols=48 Identities=29% Similarity=0.433 Sum_probs=43.3
Q ss_pred cCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 28 RKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 28 ~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
+..++.|++-|.+|+..|+..|..++||+...|..|+..++|++.-||
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVq 96 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQ 96 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhh
Confidence 345667777899999999999999999999999999999999998876
No 24
>KOG3802|consensus
Probab=98.02 E-value=1e-05 Score=54.77 Aligned_cols=47 Identities=23% Similarity=0.317 Sum_probs=44.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 29 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 29 k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
|+||+||.+.......||..|.+|.-|+..+...||.+|+|....|+
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVR 339 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVR 339 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEE
Confidence 67888999999999999999999999999999999999999987764
No 25
>KOG0847|consensus
Probab=97.98 E-value=5e-06 Score=52.77 Aligned_cols=50 Identities=32% Similarity=0.541 Sum_probs=45.8
Q ss_pred cccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 26 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 26 ~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.+.+++-.|.+|+..||..|+..|+..+|+-...|.+||-.+|+++.||+
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvk 212 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVK 212 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHH
Confidence 34566678999999999999999999999999999999999999999986
No 26
>KOG0483|consensus
Probab=97.89 E-value=1.9e-05 Score=49.36 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=41.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 31 rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.++.-+|+.+|...||..|+.++++....+..||..|||.++||.
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVa 95 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVA 95 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHH
Confidence 345557899999999999999999999999999999999999984
No 27
>KOG2252|consensus
Probab=97.72 E-value=6.3e-05 Score=52.83 Aligned_cols=51 Identities=24% Similarity=0.365 Sum_probs=46.0
Q ss_pred cccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 26 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 26 ~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
+.-+.|+.|.+||..|...|...|+.+++|+......|+.+|+|....|.|
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~N 466 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVIN 466 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHH
Confidence 344567789999999999999999999999999999999999999988865
No 28
>KOG4577|consensus
Probab=97.53 E-value=0.00012 Score=48.32 Aligned_cols=47 Identities=32% Similarity=0.439 Sum_probs=44.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 29 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 29 k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
..+|.||++|..|+..|...+...+-|..+.|+.|+..+||..+.||
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQ 212 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQ 212 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehh
Confidence 35789999999999999999999999999999999999999998876
No 29
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=96.73 E-value=0.00065 Score=32.19 Aligned_cols=26 Identities=23% Similarity=0.470 Sum_probs=20.5
Q ss_pred hcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 51 ETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 51 ~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
.++||+..++..||...||+..||.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~ 32 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISN 32 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence 36899999999999999999999864
No 30
>KOG0774|consensus
Probab=96.28 E-value=0.0072 Score=39.58 Aligned_cols=46 Identities=28% Similarity=0.461 Sum_probs=40.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 31 RRIRTTFTSAQLKELERAFQE---THYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 31 rr~Rt~~s~~q~~~Le~~F~~---~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
+|+|..|+..--..|...|.. ++||+...+++||.+-+++-+||-|
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsn 237 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSN 237 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcc
Confidence 567888999999999999864 7799999999999999999998854
No 31
>KOG0490|consensus
Probab=95.72 E-value=0.018 Score=35.92 Aligned_cols=50 Identities=44% Similarity=0.593 Sum_probs=45.0
Q ss_pred cccCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 26 EKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 26 ~~~k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
...+.++.|+.+...|+..+...|...++|+...+..|+..+++++..|+
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q 198 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQ 198 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhh
Confidence 34567788999999999999999999999999999999999999997664
No 32
>KOG0775|consensus
Probab=95.71 E-value=0.02 Score=37.70 Aligned_cols=40 Identities=23% Similarity=0.324 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 37 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 37 ~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
|...-...|..-|..++||+..++.+||..+||+..||-|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsN 222 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSN 222 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhh
Confidence 4444456788889999999999999999999999999854
No 33
>KOG1168|consensus
Probab=94.66 E-value=0.022 Score=37.95 Aligned_cols=47 Identities=28% Similarity=0.360 Sum_probs=41.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 29 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 29 k~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.+||+||....-.-..||..|...+-|+....+.+|.+|.|....|+
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVR 354 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 354 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEE
Confidence 35778899888889999999999999999999999999999876553
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=92.69 E-value=0.22 Score=24.90 Aligned_cols=38 Identities=26% Similarity=0.396 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCcchh
Q psy7107 37 FTSAQLKELERAFQETHY--PDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 37 ~s~~q~~~Le~~F~~~~y--~~~~~r~~La~~l~l~~~qV 74 (76)
+|..|...|...+....| |-...-.+||..||++..-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 478899999999999887 55556679999999998643
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=92.48 E-value=0.45 Score=23.56 Aligned_cols=40 Identities=20% Similarity=0.388 Sum_probs=29.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 31 rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
++.|..+|.++-..+-..++.+. ....+|..+|++.++|.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~ 40 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVS 40 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHH
Confidence 46788999999998888888776 46689999999998874
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=88.62 E-value=0.31 Score=24.69 Aligned_cols=35 Identities=14% Similarity=0.185 Sum_probs=24.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 42 LKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 42 ~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
+..|+..|...+++....-..|..+.+|+..||++
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~ 44 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRD 44 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHH
Confidence 45699999999999888889999999999999873
No 37
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=84.96 E-value=1.3 Score=27.72 Aligned_cols=38 Identities=18% Similarity=0.376 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCcch
Q psy7107 36 TFTSAQLKELERAFQETHY--PDIYTREEIAMKIDLTEAR 73 (76)
Q Consensus 36 ~~s~~q~~~Le~~F~~~~y--~~~~~r~~La~~l~l~~~q 73 (76)
.+|..|+..|...|....| |-...-.+||..||++..-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 6999999999999999986 5555667899999999854
No 38
>KOG1146|consensus
Probab=82.27 E-value=3.1 Score=33.06 Aligned_cols=46 Identities=24% Similarity=0.336 Sum_probs=41.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 30 ~rr~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
++..|+.++..|+..+...|....|+...+.+.|...++++.+.|+
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~ 948 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQ 948 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhH
Confidence 5678999999999999999999999999999999999999987664
No 39
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=76.93 E-value=3 Score=19.62 Aligned_cols=35 Identities=17% Similarity=0.317 Sum_probs=15.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 35 TTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 35 t~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
..+|.++...++.....+ ....++|..||.+...|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV 37 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTV 37 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHH
Confidence 456778888887665543 35668999999998765
No 40
>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=73.15 E-value=3.9 Score=20.40 Aligned_cols=32 Identities=28% Similarity=0.482 Sum_probs=21.9
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 41 QLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 41 q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
|+.-|+-.+. +.+.... +||..+|+++..|++
T Consensus 7 q~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 7 QLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 5555666666 6656544 899999999988763
No 41
>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=70.91 E-value=7.2 Score=18.44 Aligned_cols=34 Identities=21% Similarity=0.336 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 37 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 37 ~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.++.+...+...|..+ ..-.++|..+|++...|+
T Consensus 5 L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~ 38 (50)
T PF04545_consen 5 LPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVR 38 (50)
T ss_dssp S-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHH
T ss_pred CCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHH
Confidence 5667777777777333 246689999999998775
No 42
>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=70.48 E-value=13 Score=22.69 Aligned_cols=38 Identities=24% Similarity=0.434 Sum_probs=31.2
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcc
Q psy7107 33 IRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEA 72 (76)
Q Consensus 33 ~Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~ 72 (76)
....+|.+++.++...-..+ |..+.+..||.++||+..
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~ 119 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPL 119 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHH
Confidence 45789999999998766555 667889999999999874
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=69.21 E-value=7.3 Score=19.86 Aligned_cols=38 Identities=13% Similarity=0.246 Sum_probs=22.6
Q ss_pred CCCCCCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 32 RIRTTFTSAQLKELERAF-QETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 32 r~Rt~~s~~q~~~Le~~F-~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
+.|..||.++...+-... ... .....+|..+|++...+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l 40 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTL 40 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccc
Confidence 456789999888776655 322 35668899999987665
No 44
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.79 E-value=7 Score=21.72 Aligned_cols=38 Identities=21% Similarity=0.264 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 37 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 37 ~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
..++|...-...|+.+.-.+.-..+++|..|+.++..|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 45677766666666666555556678899999988544
No 45
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=60.42 E-value=16 Score=18.60 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 34 RTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 34 Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
|..|+...-...-..+....---...|+ .|.++|+++.+|+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr 43 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVR 43 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHH
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHH
Confidence 3445555444443444433333333454 4999999998886
No 46
>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=59.61 E-value=11 Score=17.29 Aligned_cols=14 Identities=50% Similarity=0.686 Sum_probs=11.6
Q ss_pred CCCHHHHHHHHHHH
Q psy7107 36 TFTSAQLKELERAF 49 (76)
Q Consensus 36 ~~s~~q~~~Le~~F 49 (76)
.||..|+..|+.-.
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 69999999998643
No 47
>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=56.51 E-value=4.1 Score=20.04 Aligned_cols=16 Identities=38% Similarity=0.580 Sum_probs=12.6
Q ss_pred HHHHHHcCCCcchhcC
Q psy7107 61 EEIAMKIDLTEARVQK 76 (76)
Q Consensus 61 ~~La~~l~l~~~qVk~ 76 (76)
.+||..+|++..||++
T Consensus 32 ~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 32 QELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHTS-HHHHHH
T ss_pred HHHHHHHCCCHHHhcc
Confidence 4789999999999863
No 48
>PRK13558 bacterio-opsin activator; Provisional
Probab=54.41 E-value=17 Score=26.15 Aligned_cols=40 Identities=23% Similarity=0.414 Sum_probs=34.1
Q ss_pred CCCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCcchh
Q psy7107 35 TTFTSAQLKELERAFQETHY--PDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 35 t~~s~~q~~~Le~~F~~~~y--~~~~~r~~La~~l~l~~~qV 74 (76)
..+|..|...|+..+....| |-...-.+||..||++..-+
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 46899999999999999997 66667789999999997543
No 49
>KOG0773|consensus
Probab=54.25 E-value=26 Score=23.45 Aligned_cols=46 Identities=17% Similarity=0.224 Sum_probs=33.5
Q ss_pred CCCCCCCCHHHHHHHHHH-Hh--hcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 31 RRIRTTFTSAQLKELERA-FQ--ETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 31 rr~Rt~~s~~q~~~Le~~-F~--~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
.|.+..+.......|+.- |+ ..+||+...+..|+..+||+..||.|
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~N 288 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSN 288 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCc
Confidence 344446667666666644 22 25699999988999999999999865
No 50
>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=52.61 E-value=25 Score=16.37 Aligned_cols=33 Identities=21% Similarity=0.420 Sum_probs=20.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 37 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 37 ~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
++.++...+...+.... ...++|..+|++...|
T Consensus 6 ~~~~~~~~i~~l~~~G~-----si~~IA~~~gvsr~Tv 38 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEGM-----SIAEIAKQFGVSRSTV 38 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHH
T ss_pred CCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHH
Confidence 45555555655555552 4668999999988765
No 51
>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=51.60 E-value=18 Score=17.22 Aligned_cols=17 Identities=18% Similarity=0.423 Sum_probs=12.4
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
...+||..++++.+.|+
T Consensus 17 t~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 17 TAKELAEELGVSRRTIR 33 (55)
T ss_dssp EHHHHHHHCTS-HHHHH
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 34589999999988765
No 52
>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=50.47 E-value=3 Score=22.19 Aligned_cols=30 Identities=30% Similarity=0.155 Sum_probs=20.8
Q ss_pred HHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 46 ERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 46 e~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
+..|...+|.......++|..+|+++..|+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk 50 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVR 50 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHH
Confidence 334555555444567789999999998775
No 53
>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=47.87 E-value=47 Score=19.64 Aligned_cols=25 Identities=8% Similarity=0.090 Sum_probs=21.1
Q ss_pred hhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 50 QETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 50 ~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
...-|++......+|..||++..+|
T Consensus 27 ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 27 EQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 3445899999999999999999876
No 54
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=46.98 E-value=48 Score=19.73 Aligned_cols=25 Identities=12% Similarity=0.098 Sum_probs=21.3
Q ss_pred hhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 50 QETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 50 ~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
....|++......+|..++++..+|
T Consensus 33 ~~~g~ip~~~~~~iA~~l~v~~~~v 57 (154)
T PRK07539 33 EQRGWVPDEAIEAVADYLGMPAIDV 57 (154)
T ss_pred HHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 4456899999999999999999876
No 55
>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=46.89 E-value=10 Score=19.40 Aligned_cols=16 Identities=25% Similarity=0.513 Sum_probs=13.6
Q ss_pred HHHHHHHcCCCcchhc
Q psy7107 60 REEIAMKIDLTEARVQ 75 (76)
Q Consensus 60 r~~La~~l~l~~~qVk 75 (76)
-..+|..||+++.+|.
T Consensus 25 lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIR 40 (60)
T ss_pred HHHHHHHHCCCHHHHH
Confidence 4578999999999885
No 56
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=46.38 E-value=52 Score=19.80 Aligned_cols=32 Identities=25% Similarity=0.159 Sum_probs=24.0
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 43 KELERAFQETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 43 ~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
..|...=+..-|++......+|..||++..+|
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 33433334456899999999999999999876
No 57
>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=45.06 E-value=12 Score=17.50 Aligned_cols=16 Identities=31% Similarity=0.501 Sum_probs=12.0
Q ss_pred HHHHHHHcCCCcchhc
Q psy7107 60 REEIAMKIDLTEARVQ 75 (76)
Q Consensus 60 r~~La~~l~l~~~qVk 75 (76)
-.+||..+|+++..|.
T Consensus 20 ~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 20 YAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 3579999999998764
No 58
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=43.76 E-value=33 Score=20.47 Aligned_cols=35 Identities=26% Similarity=0.274 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 35 TTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 35 t~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
..+++.|...|.. +..+ ....++|..||++...|+
T Consensus 5 ~~Lt~rqreVL~l-r~~G-----lTq~EIAe~LGiS~~tVs 39 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG-----LTQQEIADILGTSRANVS 39 (141)
T ss_pred cCCCHHHHHHHHH-HHcC-----CCHHHHHHHHCCCHHHHH
Confidence 4567888888876 3222 256789999999987664
No 59
>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=42.65 E-value=6.6 Score=18.76 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=14.8
Q ss_pred CCCCHHHHHHHHHHcCCCcchhc
Q psy7107 53 HYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 53 ~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.|.....-.++|..+|+++..|+
T Consensus 22 ~~~~g~s~~eIa~~l~~s~~~v~ 44 (54)
T PF08281_consen 22 RYFQGMSYAEIAEILGISESTVK 44 (54)
T ss_dssp HHTS---HHHHHHHCTS-HHHHH
T ss_pred HHHHCcCHHHHHHHHCcCHHHHH
Confidence 34445567799999999998775
No 60
>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=42.39 E-value=44 Score=19.68 Aligned_cols=33 Identities=27% Similarity=0.199 Sum_probs=21.7
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 43 KELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 43 ~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
..|...=+...|++...-..+|..++++..+|.
T Consensus 17 ~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 17 PILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 334444344568999999999999999998763
No 61
>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=40.70 E-value=21 Score=21.71 Aligned_cols=16 Identities=19% Similarity=0.459 Sum_probs=12.9
Q ss_pred HHHHHHHHcCCCcchh
Q psy7107 59 TREEIAMKIDLTEARV 74 (76)
Q Consensus 59 ~r~~La~~l~l~~~qV 74 (76)
.|.+||.+++|-++|+
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 5889999999999986
No 62
>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=40.49 E-value=43 Score=16.15 Aligned_cols=34 Identities=26% Similarity=0.373 Sum_probs=20.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 36 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 36 ~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.+|..++..|.....-. ...++|..+++++..|+
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~ 36 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVK 36 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHH
Confidence 46677777665544433 45677888888776653
No 63
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=39.70 E-value=74 Score=19.51 Aligned_cols=25 Identities=20% Similarity=0.114 Sum_probs=20.9
Q ss_pred hhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 50 QETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 50 ~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
...-|++......+|..||++..+|
T Consensus 47 ~~~GyIp~e~~~~iA~~l~v~~a~V 71 (169)
T PRK07571 47 ELFGYLERDLLLYVARQLKLPLSRV 71 (169)
T ss_pred HHcCCCCHHHHHHHHHHhCcCHHHH
Confidence 3445888888899999999999876
No 64
>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=39.67 E-value=34 Score=18.34 Aligned_cols=18 Identities=11% Similarity=0.359 Sum_probs=14.0
Q ss_pred HHHHHHHHHcCCCcchhc
Q psy7107 58 YTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 58 ~~r~~La~~l~l~~~qVk 75 (76)
..-.+++++|||++.+|.
T Consensus 12 ~~wk~~~R~LGlse~~Id 29 (80)
T cd08313 12 RRWKEFVRRLGLSDNEIE 29 (80)
T ss_pred HHHHHHHHHcCCCHHHHH
Confidence 345679999999997763
No 65
>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=39.61 E-value=51 Score=18.18 Aligned_cols=31 Identities=16% Similarity=0.304 Sum_probs=19.4
Q ss_pred HHHHHHhhc-CCCCHHHHHHHHHHcCCCcchh
Q psy7107 44 ELERAFQET-HYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 44 ~Le~~F~~~-~y~~~~~r~~La~~l~l~~~qV 74 (76)
.|...|..- ...+...-..|++.|||++..|
T Consensus 5 ~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I 36 (96)
T cd08315 5 TLRRSFDHFIKEVPFDSWNRLMRQLGLSENEI 36 (96)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHH
Confidence 344455443 2233445668999999998765
No 66
>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=39.45 E-value=40 Score=15.00 Aligned_cols=34 Identities=18% Similarity=0.242 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 37 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 37 ~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
++..+...+...+. .......+|..+|++...|+
T Consensus 11 l~~~~~~~~~~~~~-----~~~~~~~ia~~~~~s~~~i~ 44 (55)
T cd06171 11 LPEREREVILLRFG-----EGLSYEEIAEILGISRSTVR 44 (55)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHH
Confidence 34555555554432 22245678999999987764
No 67
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=39.44 E-value=14 Score=20.40 Aligned_cols=28 Identities=21% Similarity=0.368 Sum_probs=19.0
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 44 ELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 44 ~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
+|...|...-+. .+.+|..|+++...|.
T Consensus 14 ELq~nf~~~~ls----~~~ia~dL~~s~~~le 41 (89)
T PF10078_consen 14 ELQANFELSGLS----LEQIAADLGTSPEHLE 41 (89)
T ss_pred HHHHHHHHcCCC----HHHHHHHhCCCHHHHH
Confidence 566666666543 5577888888887654
No 68
>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=38.75 E-value=65 Score=18.22 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=14.3
Q ss_pred HHHHHHHHcCCCcchhcC
Q psy7107 59 TREEIAMKIDLTEARVQK 76 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk~ 76 (76)
.-.++|..||+++..|++
T Consensus 125 s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 125 KEIDIAKKLHISRQSVYK 142 (142)
T ss_pred CHHHHHHHHCcCHHhhcC
Confidence 345789999999988875
No 69
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=38.22 E-value=79 Score=19.37 Aligned_cols=36 Identities=31% Similarity=0.223 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 39 SAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 39 ~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
..-+..|.......-|.+...-..+|..|+++...|
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 445666777777777999999999999999998765
No 70
>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=37.42 E-value=69 Score=17.14 Aligned_cols=33 Identities=9% Similarity=0.260 Sum_probs=21.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 36 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 36 ~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
+.|.+|+..+....- ..-..||..||+++..|.
T Consensus 4 ~~t~~~l~~ia~~iG-------~~Wk~Lar~LGls~~dI~ 36 (86)
T cd08318 4 PVTGEQITVFANKLG-------EDWKTLAPHLEMKDKEIR 36 (86)
T ss_pred CCCHHHHHHHHHHHh-------hhHHHHHHHcCCCHHHHH
Confidence 346677776643221 245579999999987653
No 71
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=34.51 E-value=54 Score=18.71 Aligned_cols=18 Identities=33% Similarity=0.386 Sum_probs=14.4
Q ss_pred HHHHHHHHHcCCCcchhc
Q psy7107 58 YTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 58 ~~r~~La~~l~l~~~qVk 75 (76)
..-.++|..+|++...|+
T Consensus 123 ~s~~EIA~~l~is~~tV~ 140 (154)
T PRK06759 123 KTMGEIALETEMTYYQVR 140 (154)
T ss_pred CCHHHHHHHHCCCHHHHH
Confidence 356688999999998775
No 72
>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=34.21 E-value=55 Score=19.32 Aligned_cols=17 Identities=29% Similarity=0.456 Sum_probs=13.2
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|+++..|+
T Consensus 118 s~~eIA~~lgis~~tV~ 134 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAK 134 (170)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45678889999987775
No 73
>KOG4565|consensus
Probab=33.36 E-value=94 Score=19.52 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=16.5
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHH
Q psy7107 27 KRKQRRIRTTFTSAQLKELERAF 49 (76)
Q Consensus 27 ~~k~rr~Rt~~s~~q~~~Le~~F 49 (76)
.+++|++|-+|....-+.||...
T Consensus 109 sKqpRkKRGrYRqYd~eileEAi 131 (206)
T KOG4565|consen 109 SKQPRKKRGRYRQYDKEILEEAI 131 (206)
T ss_pred ccCccccccchhhhhHHHHHHHH
Confidence 45667777778888777787664
No 74
>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=32.68 E-value=15 Score=20.52 Aligned_cols=17 Identities=29% Similarity=0.393 Sum_probs=11.9
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
...+||.+.||++.+|.
T Consensus 74 n~~eLA~kyglS~r~I~ 90 (108)
T PF08765_consen 74 NVRELARKYGLSERQIY 90 (108)
T ss_dssp -HHHHHHHHT--HHHHH
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 45689999999998874
No 75
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.63 E-value=65 Score=18.57 Aligned_cols=17 Identities=24% Similarity=0.370 Sum_probs=13.3
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|+++..|+
T Consensus 124 s~~EIA~~lgis~~tV~ 140 (160)
T PRK09642 124 SYQEIALQEKIEVKTVE 140 (160)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 34578889999988775
No 76
>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=30.90 E-value=8 Score=19.46 Aligned_cols=17 Identities=24% Similarity=0.341 Sum_probs=13.4
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..||++...|.
T Consensus 15 ~~~eIA~~Lg~~~~TV~ 31 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVY 31 (58)
T ss_pred CHHHHHHHHCCChHHHH
Confidence 45688999999987764
No 77
>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=30.46 E-value=72 Score=18.93 Aligned_cols=36 Identities=33% Similarity=0.424 Sum_probs=25.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 34 RTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 34 Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
.+.++..|...+... ... ....++|..+|++...|+
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G-----lTq~EIAe~LgiS~stV~ 39 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG-----LSQKEIAKELKTTRANVS 39 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCcCHHHHH
Confidence 356778888888763 222 256789999999987764
No 78
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=30.35 E-value=61 Score=18.50 Aligned_cols=33 Identities=18% Similarity=0.173 Sum_probs=21.6
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 41 QLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 41 q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
+...|...|... +....-.+||..+.++++.|+
T Consensus 5 ~y~~L~~~~~~~--~~~vtl~elA~~l~cS~Rn~r 37 (115)
T PF12793_consen 5 QYQRLWQHYGGQ--PVEVTLDELAELLFCSRRNAR 37 (115)
T ss_pred HHHHHHHHcCCC--CcceeHHHHHHHhCCCHHHHH
Confidence 445566555522 333455689999999998775
No 79
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=30.02 E-value=16 Score=22.64 Aligned_cols=35 Identities=9% Similarity=0.127 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 36 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 36 ~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
.+|+.++..|.-.-+- ....++|.+|++++..|++
T Consensus 137 ~LT~RE~eVL~lla~G------~snkeIA~~L~iS~~TVk~ 171 (207)
T PRK15411 137 SLSRTESSMLRMWMAG------QGTIQISDQMNIKAKTVSS 171 (207)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHH
Confidence 3788888777543322 2456899999999988763
No 80
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=29.82 E-value=29 Score=17.72 Aligned_cols=17 Identities=35% Similarity=0.503 Sum_probs=12.8
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
...+||..+|++...|+
T Consensus 22 t~eEiA~~lgis~~~v~ 38 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVR 38 (78)
T ss_dssp BHHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHcccHHHHH
Confidence 55689999999987764
No 81
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=29.39 E-value=60 Score=20.11 Aligned_cols=40 Identities=15% Similarity=0.274 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 36 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 36 ~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
.+|..++..+......+ +-....-.++|..+++++..|++
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~ 197 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRK 197 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHH
Confidence 35666666554444322 33344567899999999988864
No 82
>PF13730 HTH_36: Helix-turn-helix domain
Probab=29.30 E-value=36 Score=16.13 Aligned_cols=18 Identities=22% Similarity=0.364 Sum_probs=13.8
Q ss_pred HHHHHHHHHcCCCcchhc
Q psy7107 58 YTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 58 ~~r~~La~~l~l~~~qVk 75 (76)
+....||..+|++...|+
T Consensus 26 pS~~~la~~~g~s~~Tv~ 43 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQ 43 (55)
T ss_pred cCHHHHHHHHCcCHHHHH
Confidence 346688999999987765
No 83
>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=29.24 E-value=77 Score=18.12 Aligned_cols=18 Identities=17% Similarity=0.093 Sum_probs=13.6
Q ss_pred HHHHHHHHHcCCCcchhc
Q psy7107 58 YTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 58 ~~r~~La~~l~l~~~qVk 75 (76)
..-.++|..+|++...|+
T Consensus 128 ~~~~eIA~~l~is~~tv~ 145 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVY 145 (159)
T ss_pred CCHHHHHHHhCCCHHHHH
Confidence 345678889999987765
No 84
>PRK04217 hypothetical protein; Provisional
Probab=29.20 E-value=77 Score=18.09 Aligned_cols=37 Identities=19% Similarity=0.178 Sum_probs=24.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhc
Q psy7107 34 RTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 34 Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk 75 (76)
-...+.+|...+...+.... ...++|..+|++...|+
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~ 76 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVW 76 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHH
Confidence 34467777766655443332 45689999999987764
No 85
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.78 E-value=97 Score=18.39 Aligned_cols=17 Identities=24% Similarity=0.464 Sum_probs=13.5
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..||+++..|+
T Consensus 145 s~~EIA~~lgis~~tVk 161 (178)
T PRK12529 145 KQKDIAQALDIALPTVK 161 (178)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999988775
No 86
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=28.78 E-value=79 Score=18.10 Aligned_cols=17 Identities=24% Similarity=0.270 Sum_probs=13.5
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..||++...|+
T Consensus 124 s~~EIA~~lgis~~tV~ 140 (161)
T PRK09047 124 DVAETAAAMGCSEGSVK 140 (161)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 35688999999988776
No 87
>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=27.72 E-value=82 Score=18.54 Aligned_cols=17 Identities=35% Similarity=0.366 Sum_probs=13.3
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|+++..|+
T Consensus 152 s~~EIA~~lgis~~tVk 168 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVE 168 (183)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 45678888999988776
No 88
>KOG0041|consensus
Probab=27.59 E-value=1.4e+02 Score=19.32 Aligned_cols=37 Identities=19% Similarity=0.413 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHcCCCcc
Q psy7107 36 TFTSAQLKELERAFQE-----THYPDIYTREEIAMKIDLTEA 72 (76)
Q Consensus 36 ~~s~~q~~~Le~~F~~-----~~y~~~~~r~~La~~l~l~~~ 72 (76)
-|+..|+..++..|.. .-|++..+-.....+||.+..
T Consensus 92 eFsrkqIk~~~~~Fk~yDe~rDgfIdl~ELK~mmEKLgapQT 133 (244)
T KOG0041|consen 92 EFSRKQIKDAESMFKQYDEDRDGFIDLMELKRMMEKLGAPQT 133 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHhCCchh
Confidence 3788899999999854 568999988889999998864
No 89
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=27.51 E-value=76 Score=18.40 Aligned_cols=17 Identities=29% Similarity=0.255 Sum_probs=13.2
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 146 s~~eIA~~lgis~~tV~ 162 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVR 162 (182)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 34578999999988775
No 90
>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=27.44 E-value=55 Score=17.56 Aligned_cols=16 Identities=25% Similarity=0.524 Sum_probs=13.0
Q ss_pred HHHHHHHHcCCCcchh
Q psy7107 59 TREEIAMKIDLTEARV 74 (76)
Q Consensus 59 ~r~~La~~l~l~~~qV 74 (76)
.-..||+.||+++.+|
T Consensus 15 ~Wk~laR~LGlse~~I 30 (86)
T cd08306 15 DWRKLARKLGLSETKI 30 (86)
T ss_pred hHHHHHHHcCCCHHHH
Confidence 4567999999999765
No 91
>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=26.80 E-value=55 Score=12.77 Aligned_cols=33 Identities=21% Similarity=0.393 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchh
Q psy7107 37 FTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74 (76)
Q Consensus 37 ~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qV 74 (76)
++..+...+...+.... ....+|..++++...|
T Consensus 6 ~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv 38 (42)
T cd00569 6 LTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTL 38 (42)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHH
Confidence 45565555555554322 3447788888887655
No 92
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=26.31 E-value=91 Score=18.76 Aligned_cols=17 Identities=24% Similarity=0.348 Sum_probs=13.2
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..||++...|+
T Consensus 160 s~~EIA~~Lgis~~tVk 176 (194)
T PRK09646 160 TYREVAERLAVPLGTVK 176 (194)
T ss_pred CHHHHHHHhCCChHhHH
Confidence 45678888999888775
No 93
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.18 E-value=90 Score=18.63 Aligned_cols=17 Identities=24% Similarity=0.427 Sum_probs=12.9
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 149 s~~eIA~~lgis~~tV~ 165 (189)
T PRK12515 149 SVEEVGEIVGIPESTVK 165 (189)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 34578888999887775
No 94
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=26.15 E-value=1.2e+02 Score=17.48 Aligned_cols=17 Identities=24% Similarity=0.433 Sum_probs=13.3
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
...++|..+|++...|+
T Consensus 127 s~~EIA~~lgis~~tV~ 143 (163)
T PRK07037 127 TQKDIARELGVSPTLVN 143 (163)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999987775
No 95
>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=25.43 E-value=92 Score=17.95 Aligned_cols=17 Identities=29% Similarity=0.290 Sum_probs=13.0
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..||+++..|+
T Consensus 140 s~~eIA~~l~is~~tv~ 156 (170)
T TIGR02952 140 PIAEVARILGKTEGAVK 156 (170)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45678888999887765
No 96
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=25.17 E-value=84 Score=15.52 Aligned_cols=14 Identities=14% Similarity=0.311 Sum_probs=8.9
Q ss_pred HHHHHcCCCcchhc
Q psy7107 62 EIAMKIDLTEARVQ 75 (76)
Q Consensus 62 ~La~~l~l~~~qVk 75 (76)
+.|..||+....+|
T Consensus 20 eAA~~Lgv~~T~LK 33 (52)
T PF02042_consen 20 EAAKELGVSVTTLK 33 (52)
T ss_pred HHHHHhCCCHHHHH
Confidence 45777777765544
No 97
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=24.51 E-value=83 Score=18.20 Aligned_cols=36 Identities=22% Similarity=0.346 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCc
Q psy7107 36 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTE 71 (76)
Q Consensus 36 ~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~ 71 (76)
..+..-..+|+..|....---..-|.+||.++|+.+
T Consensus 95 flsesgmeelqdrfmns~st~yrwrke~a~kfgvr~ 130 (143)
T PRK15183 95 FLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVRE 130 (143)
T ss_pred hhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCC
Confidence 345566677887776654333344789999998865
No 98
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=24.18 E-value=1e+02 Score=18.87 Aligned_cols=18 Identities=17% Similarity=0.433 Sum_probs=13.7
Q ss_pred HHHHHHHHHcCCCcchhc
Q psy7107 58 YTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 58 ~~r~~La~~l~l~~~qVk 75 (76)
..-.++|..+|+++..|+
T Consensus 170 ~s~~EIA~~lgis~~tV~ 187 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVK 187 (206)
T ss_pred CCHHHHHHHHCCCHHHHH
Confidence 345678889999987775
No 99
>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=24.18 E-value=81 Score=16.57 Aligned_cols=19 Identities=11% Similarity=0.289 Sum_probs=14.2
Q ss_pred HHHHHHHHHHcCCCcchhc
Q psy7107 57 IYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 57 ~~~r~~La~~l~l~~~qVk 75 (76)
...-..||+.||+++..|.
T Consensus 11 ~~~Wk~laR~LGls~~~I~ 29 (79)
T cd08784 11 FDQHKRFFRKLGLSDNEIK 29 (79)
T ss_pred HHHHHHHHHHcCCCHHHHH
Confidence 3445689999999987653
No 100
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=24.05 E-value=1.1e+02 Score=17.89 Aligned_cols=17 Identities=24% Similarity=0.468 Sum_probs=13.1
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..||+++..|+
T Consensus 136 s~~EIA~~lgis~~tV~ 152 (173)
T PRK09645 136 STAQIAADLGIPEGTVK 152 (173)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 35678889999987775
No 101
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=24.03 E-value=1.1e+02 Score=18.12 Aligned_cols=17 Identities=24% Similarity=0.354 Sum_probs=13.3
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 151 s~~eIA~~lgis~~tV~ 167 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVK 167 (182)
T ss_pred CHHHHHHHHCCChhhHH
Confidence 45578889999988776
No 102
>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=23.97 E-value=1.1e+02 Score=17.28 Aligned_cols=17 Identities=24% Similarity=0.391 Sum_probs=13.4
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
...++|..+|+++..|+
T Consensus 131 ~~~eIA~~lgis~~tv~ 147 (161)
T TIGR02985 131 SYKEIAEELGISVKTVE 147 (161)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45678899999988775
No 103
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=23.92 E-value=1.1e+02 Score=16.44 Aligned_cols=31 Identities=23% Similarity=0.225 Sum_probs=17.9
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 44 ELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 44 ~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
.|-..|....-|-.. ..||..+++++..|+|
T Consensus 12 alV~~Y~~~~~PVgS--k~ia~~l~~s~aTIRN 42 (78)
T PF03444_consen 12 ALVELYIETGEPVGS--KTIAEELGRSPATIRN 42 (78)
T ss_pred HHHHHHHhcCCCcCH--HHHHHHHCCChHHHHH
Confidence 334445555444333 2567778888877765
No 104
>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=23.89 E-value=1e+02 Score=17.98 Aligned_cols=17 Identities=35% Similarity=0.376 Sum_probs=13.4
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 137 s~~eiA~~lgis~~tv~ 153 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVK 153 (169)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45678999999988775
No 105
>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=23.80 E-value=95 Score=17.85 Aligned_cols=17 Identities=12% Similarity=0.339 Sum_probs=13.6
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 128 s~~eIA~~lgis~~tV~ 144 (162)
T TIGR02983 128 SEAQVAEALGISVGTVK 144 (162)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 35678999999988776
No 106
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=23.75 E-value=1.3e+02 Score=17.90 Aligned_cols=17 Identities=29% Similarity=0.304 Sum_probs=13.5
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 157 s~~EIA~~lgis~~tV~ 173 (189)
T PRK09648 157 SAEETAEAVGSTPGAVR 173 (189)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999987765
No 107
>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=23.73 E-value=70 Score=17.23 Aligned_cols=16 Identities=13% Similarity=0.466 Sum_probs=13.1
Q ss_pred HHHHHHHHcCCCcchh
Q psy7107 59 TREEIAMKIDLTEARV 74 (76)
Q Consensus 59 ~r~~La~~l~l~~~qV 74 (76)
.-..||..||+++..|
T Consensus 15 ~W~~Lar~Lgls~~~I 30 (83)
T cd08319 15 EWEQVLLDLGLSQTDI 30 (83)
T ss_pred hHHHHHHHcCCCHHHH
Confidence 4567999999999765
No 108
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.44 E-value=1e+02 Score=17.72 Aligned_cols=17 Identities=29% Similarity=0.417 Sum_probs=13.0
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|+++..|+
T Consensus 129 s~~eIA~~lgis~~tV~ 145 (166)
T PRK09639 129 SYKEIAEALGIKESSVG 145 (166)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45678888898887775
No 109
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=23.39 E-value=1.2e+02 Score=15.41 Aligned_cols=32 Identities=38% Similarity=0.436 Sum_probs=18.2
Q ss_pred CCHHHHHHHHH---HHhhcCCCCHHHHHHHHHHcCCC
Q psy7107 37 FTSAQLKELER---AFQETHYPDIYTREEIAMKIDLT 70 (76)
Q Consensus 37 ~s~~q~~~Le~---~F~~~~y~~~~~r~~La~~l~l~ 70 (76)
+|..|...|+- ....+-||+ ...+||..+|+.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~ 38 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPP--TVREIAEALGLK 38 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSS
T ss_pred CCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCC
Confidence 45556555543 345566775 445899999997
No 110
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=23.25 E-value=1e+02 Score=18.65 Aligned_cols=18 Identities=33% Similarity=0.532 Sum_probs=14.2
Q ss_pred HHHHHHHHHcCCCcchhc
Q psy7107 58 YTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 58 ~~r~~La~~l~l~~~qVk 75 (76)
....++|..+|+++..|+
T Consensus 152 ls~~EIA~~lgiS~~tV~ 169 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVR 169 (185)
T ss_pred CCHHHHHHHHCcCHHHHH
Confidence 356688999999998775
No 111
>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=22.71 E-value=82 Score=16.88 Aligned_cols=16 Identities=13% Similarity=0.320 Sum_probs=12.9
Q ss_pred HHHHHHHHcCCCcchh
Q psy7107 59 TREEIAMKIDLTEARV 74 (76)
Q Consensus 59 ~r~~La~~l~l~~~qV 74 (76)
.-..||..||+++..|
T Consensus 15 ~Wk~lar~LGlse~~I 30 (86)
T cd08779 15 DWQAIGLHLGLSYREL 30 (86)
T ss_pred HHHHHHHHcCCCHHHH
Confidence 4568999999998765
No 112
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=22.70 E-value=1.1e+02 Score=18.01 Aligned_cols=17 Identities=29% Similarity=0.475 Sum_probs=13.4
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 149 s~~eIA~~l~is~~tV~ 165 (184)
T PRK12512 149 SIKETAAKLSMSEGAVR 165 (184)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 45678999999987775
No 113
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.67 E-value=1.2e+02 Score=17.71 Aligned_cols=17 Identities=12% Similarity=0.118 Sum_probs=13.5
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|+++..|+
T Consensus 130 s~~eIA~~lgis~~tV~ 146 (164)
T PRK12547 130 SYEDAAAICGCAVGTIK 146 (164)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 45688999999988775
No 114
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.47 E-value=1.2e+02 Score=17.76 Aligned_cols=17 Identities=18% Similarity=0.288 Sum_probs=13.7
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|+++..|+
T Consensus 147 s~~eIA~~lgis~~tV~ 163 (179)
T PRK12514 147 SYKELAERHDVPLNTMR 163 (179)
T ss_pred CHHHHHHHHCCChHHHH
Confidence 45688999999998776
No 115
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. 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 sign
Probab=21.88 E-value=1.1e+02 Score=17.01 Aligned_cols=17 Identities=18% Similarity=0.284 Sum_probs=13.4
Q ss_pred HHHHHHHHHcCCCcchh
Q psy7107 58 YTREEIAMKIDLTEARV 74 (76)
Q Consensus 58 ~~r~~La~~l~l~~~qV 74 (76)
..-.++|+.+||++..|
T Consensus 21 ~~wK~faR~lglse~~I 37 (97)
T cd08316 21 KDVKKFVRKSGLSEPKI 37 (97)
T ss_pred HHHHHHHHHcCCCHHHH
Confidence 45567999999999765
No 116
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=21.88 E-value=1.1e+02 Score=17.61 Aligned_cols=17 Identities=24% Similarity=0.278 Sum_probs=13.5
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 143 ~~~eIA~~lgis~~tv~ 159 (179)
T PRK11924 143 SYREIAEILGVPVGTVK 159 (179)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999988775
No 117
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (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. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=21.88 E-value=58 Score=16.49 Aligned_cols=17 Identities=18% Similarity=0.462 Sum_probs=13.1
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-..||..||+++..|.
T Consensus 12 ~W~~la~~Lgl~~~~I~ 28 (79)
T cd01670 12 DWKKLARKLGLSDGEID 28 (79)
T ss_pred HHHHHHHHhCCCHHHHH
Confidence 45579999999987664
No 118
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=21.73 E-value=1.3e+02 Score=17.36 Aligned_cols=17 Identities=35% Similarity=0.387 Sum_probs=12.5
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 130 s~~eIA~~lgis~~tv~ 146 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVK 146 (161)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 34578888888887665
No 119
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=21.51 E-value=67 Score=17.32 Aligned_cols=17 Identities=24% Similarity=0.397 Sum_probs=13.5
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-..||..||+++..|.
T Consensus 15 ~Wk~lar~LG~s~~eI~ 31 (86)
T cd08777 15 KWKRCARKLGFTESEIE 31 (86)
T ss_pred HHHHHHHHcCCCHHHHH
Confidence 45689999999987654
No 120
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.35 E-value=1.1e+02 Score=18.27 Aligned_cols=17 Identities=6% Similarity=0.046 Sum_probs=13.2
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|+++..|+
T Consensus 148 s~~EIA~~lgis~~tVk 164 (185)
T PRK09649 148 SYADAAAVCGCPVGTIR 164 (185)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 34678899999987775
No 121
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=21.31 E-value=1.5e+02 Score=17.79 Aligned_cols=17 Identities=18% Similarity=0.462 Sum_probs=13.7
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|+++..|+
T Consensus 152 s~~EIA~~lgis~~tVk 168 (189)
T PRK12530 152 SSEQICQECDISTSNLH 168 (189)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999998775
No 122
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=20.95 E-value=34 Score=21.97 Aligned_cols=37 Identities=16% Similarity=0.079 Sum_probs=26.1
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcchhcC
Q psy7107 34 RTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76 (76)
Q Consensus 34 Rt~~s~~q~~~Le~~F~~~~y~~~~~r~~La~~l~l~~~qVk~ 76 (76)
-..+|+.+...|+-.-+ +..-.++|..|++++..|++
T Consensus 141 ~~~LS~RE~eVL~Lia~------G~SnkEIA~~L~IS~~TVk~ 177 (217)
T PRK13719 141 KNKVTKYQNDVFILYSF------GFSHEYIAQLLNITVGSSKN 177 (217)
T ss_pred cCCCCHHHHHHHHHHHC------CCCHHHHHHHhCCCHHHHHH
Confidence 34578888877754333 22456899999999988864
No 123
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.93 E-value=36 Score=15.74 Aligned_cols=17 Identities=24% Similarity=0.393 Sum_probs=12.0
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
...++|..+|++...|.
T Consensus 19 s~~~ia~~lgvs~~Tv~ 35 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVY 35 (50)
T ss_dssp -HHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 45688999999987764
No 124
>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=20.83 E-value=1.2e+02 Score=16.52 Aligned_cols=17 Identities=24% Similarity=0.341 Sum_probs=13.0
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|+++..|.
T Consensus 128 s~~eIA~~l~~s~~~v~ 144 (158)
T TIGR02937 128 SYKEIAEILGISVGTVK 144 (158)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999887664
No 125
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=20.65 E-value=1.3e+02 Score=18.10 Aligned_cols=17 Identities=18% Similarity=0.292 Sum_probs=13.2
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 152 s~~EIA~~lg~s~~tV~ 168 (192)
T PRK09643 152 SVADAARMLGVAEGTVK 168 (192)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 45578888999888776
No 126
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=20.41 E-value=1.2e+02 Score=18.60 Aligned_cols=39 Identities=26% Similarity=0.221 Sum_probs=26.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHcCC
Q psy7107 31 RRIRTTFTSAQLKELERAFQE-----THYPDIYTREEIAMKIDL 69 (76)
Q Consensus 31 rr~Rt~~s~~q~~~Le~~F~~-----~~y~~~~~r~~La~~l~l 69 (76)
-+..+.|+.+|+.+|...|+. .-+++...-..+-+.+|.
T Consensus 8 ~~~~~~~t~~qi~~lkeaF~l~D~d~~G~I~~~el~~ilr~lg~ 51 (160)
T COG5126 8 LLTFTQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSLGF 51 (160)
T ss_pred hhhcccCCHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHcCC
Confidence 346788999999999999865 335555554444444444
No 127
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.21 E-value=1e+02 Score=18.17 Aligned_cols=20 Identities=35% Similarity=0.386 Sum_probs=15.0
Q ss_pred CHHHHHHHHHHcCCCcchhc
Q psy7107 56 DIYTREEIAMKIDLTEARVQ 75 (76)
Q Consensus 56 ~~~~r~~La~~l~l~~~qVk 75 (76)
....-.++|..+|++...|+
T Consensus 134 ~g~s~~EIA~~lgis~~tV~ 153 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVK 153 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHH
Confidence 33346688999999988775
No 128
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=20.12 E-value=1.2e+02 Score=18.01 Aligned_cols=17 Identities=18% Similarity=0.278 Sum_probs=13.2
Q ss_pred HHHHHHHHcCCCcchhc
Q psy7107 59 TREEIAMKIDLTEARVQ 75 (76)
Q Consensus 59 ~r~~La~~l~l~~~qVk 75 (76)
.-.++|..+|++...|+
T Consensus 146 s~~EIA~~lgis~~tV~ 162 (186)
T PRK05602 146 SNIEAAAVMDISVDALE 162 (186)
T ss_pred CHHHHHHHhCcCHHHHH
Confidence 34578899999987775
No 129
>PRK15372 pathogenicity island 2 effector protein SseI; Provisional
Probab=20.04 E-value=80 Score=21.02 Aligned_cols=30 Identities=27% Similarity=0.344 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHH
Q psy7107 37 FTSAQLKELERAFQETHYPDIYTREEIAMK 66 (76)
Q Consensus 37 ~s~~q~~~Le~~F~~~~y~~~~~r~~La~~ 66 (76)
++..|-..|+..|..+|.+....+++++..
T Consensus 12 csTHq~EAl~CI~~LcHP~~gtTpe~I~s~ 41 (292)
T PRK15372 12 CSTHQTEALECIWTICHPPAGTTREDVVSR 41 (292)
T ss_pred ccccHHHHHHHHHHHhCCCCCCCHHHHHHH
Confidence 567888999999999999877666666554
Done!