Query psy4349
Match_columns 80
No_of_seqs 144 out of 1121
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 23:18:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4349.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4349hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01565 homeo_ZF_HD homeobox 99.4 5.1E-13 1.1E-17 68.1 5.0 45 36-80 2-50 (58)
2 KOG0488|consensus 99.4 4.2E-13 9.1E-18 88.0 6.0 51 30-80 167-217 (309)
3 KOG0484|consensus 99.4 1.8E-13 4E-18 76.6 1.0 49 32-80 14-62 (125)
4 KOG2251|consensus 99.3 1.4E-12 2.9E-17 81.4 4.5 51 30-80 32-82 (228)
5 KOG0842|consensus 99.3 4.6E-12 1E-16 82.7 6.7 50 31-80 149-198 (307)
6 KOG0850|consensus 99.3 1.6E-12 3.5E-17 81.5 3.9 51 30-80 117-167 (245)
7 KOG0843|consensus 99.3 3.3E-12 7.2E-17 77.6 3.9 48 33-80 100-147 (197)
8 KOG0489|consensus 99.3 2.5E-12 5.4E-17 82.8 2.9 48 33-80 157-204 (261)
9 KOG0485|consensus 99.2 3.4E-11 7.3E-16 75.3 4.5 49 32-80 101-149 (268)
10 PF00046 Homeobox: Homeobox do 99.2 3.1E-11 6.7E-16 61.1 3.5 45 36-80 1-45 (57)
11 KOG0494|consensus 99.1 1.6E-10 3.5E-15 73.9 6.2 47 34-80 140-186 (332)
12 KOG0487|consensus 99.1 2.9E-10 6.2E-15 74.4 6.0 51 30-80 230-280 (308)
13 KOG0486|consensus 99.1 1.4E-10 3E-15 75.7 3.9 48 33-80 110-157 (351)
14 KOG0493|consensus 99.0 3.1E-10 6.6E-15 72.8 4.5 45 36-80 247-291 (342)
15 smart00389 HOX Homeodomain. DN 99.0 4.7E-10 1E-14 56.3 4.4 44 37-80 2-45 (56)
16 KOG0492|consensus 99.0 4.4E-10 9.5E-15 69.9 4.3 50 31-80 140-189 (246)
17 cd00086 homeodomain Homeodomai 98.9 1.8E-09 3.9E-14 54.6 4.1 44 37-80 2-45 (59)
18 KOG0491|consensus 98.9 2.9E-10 6.2E-15 68.5 -0.6 48 33-80 98-145 (194)
19 KOG0848|consensus 98.8 2.6E-09 5.6E-14 68.7 2.5 47 34-80 198-244 (317)
20 KOG0844|consensus 98.7 7.5E-09 1.6E-13 67.7 2.6 49 32-80 178-226 (408)
21 KOG3802|consensus 98.6 2E-08 4.3E-13 67.4 2.8 47 34-80 293-339 (398)
22 KOG0490|consensus 98.6 3.5E-08 7.6E-13 61.8 2.7 49 32-80 57-105 (235)
23 COG5576 Homeodomain-containing 98.6 1.3E-07 2.9E-12 56.9 5.0 48 33-80 49-96 (156)
24 KOG0849|consensus 98.6 1E-07 2.2E-12 63.9 4.4 51 30-80 171-221 (354)
25 KOG4577|consensus 98.1 6E-06 1.3E-10 54.0 3.9 47 34-80 166-212 (383)
26 KOG2252|consensus 97.9 1.8E-05 3.8E-10 55.4 4.1 47 33-79 418-464 (558)
27 KOG0483|consensus 97.8 3.1E-05 6.8E-10 48.3 3.6 44 37-80 52-95 (198)
28 KOG0847|consensus 97.4 8.8E-05 1.9E-09 47.0 1.9 48 33-80 165-212 (288)
29 KOG1168|consensus 97.1 0.00026 5.6E-09 46.6 1.5 46 35-80 309-354 (385)
30 KOG0774|consensus 96.9 0.0012 2.5E-08 43.0 3.3 44 36-79 189-235 (334)
31 KOG0775|consensus 96.8 0.0023 5E-08 41.8 3.8 38 42-79 183-220 (304)
32 PF05920 Homeobox_KN: Homeobox 96.8 0.00074 1.6E-08 31.8 1.2 24 56-79 7-30 (40)
33 KOG0490|consensus 96.6 0.0028 6E-08 39.6 3.5 51 30-80 148-198 (235)
34 KOG1146|consensus 95.4 0.029 6.2E-07 43.5 4.4 48 33-80 901-948 (1406)
35 PF04967 HTH_10: HTH DNA bindi 94.1 0.062 1.3E-06 26.8 2.3 37 42-78 1-39 (53)
36 PF04218 CENP-B_N: CENP-B N-te 93.3 0.27 5.8E-06 24.3 3.8 39 36-79 1-39 (53)
37 COG3413 Predicted DNA binding 89.8 0.33 7.1E-06 30.4 2.4 38 41-78 155-194 (215)
38 PF11569 Homez: Homeodomain le 82.3 0.67 1.5E-05 23.4 0.8 34 47-80 10-43 (56)
39 PF13936 HTH_38: Helix-turn-he 74.1 2.4 5.2E-05 19.9 1.3 35 40-79 3-37 (44)
40 PF04545 Sigma70_r4: Sigma-70, 73.3 3.3 7.1E-05 19.6 1.7 34 41-79 4-37 (50)
41 KOG0773|consensus 70.4 7.7 0.00017 26.0 3.5 45 35-79 239-286 (342)
42 PF08280 HTH_Mga: M protein tr 69.4 3.2 6.9E-05 20.7 1.2 32 45-80 6-37 (59)
43 COG4367 Uncharacterized protei 62.1 7.9 0.00017 21.4 1.9 37 42-78 3-39 (97)
44 PRK13558 bacterio-opsin activa 60.1 9 0.0002 27.6 2.5 39 40-78 606-646 (665)
45 PF08880 QLQ: QLQ; InterPro: 58.8 12 0.00025 17.2 1.9 15 41-55 2-16 (37)
46 PRK15183 Vi polysaccharide bio 57.8 12 0.00025 21.6 2.2 38 40-77 94-131 (143)
47 PF12824 MRP-L20: Mitochondria 56.9 25 0.00053 21.5 3.6 38 38-77 82-119 (164)
48 KOG3623|consensus 56.3 12 0.00027 28.4 2.6 34 47-80 568-601 (1007)
49 PF02796 HTH_7: Helix-turn-hel 55.0 14 0.00031 17.2 2.0 34 41-79 5-38 (45)
50 PF01527 HTH_Tnp_1: Transposas 54.6 22 0.00048 18.0 2.8 37 37-78 2-39 (76)
51 COG1905 NuoE NADH:ubiquinone o 50.3 32 0.00069 21.0 3.3 36 44-79 25-60 (160)
52 PRK03975 tfx putative transcri 49.5 19 0.00041 21.5 2.3 34 40-79 5-38 (141)
53 PF00196 GerE: Bacterial regul 49.1 16 0.00034 17.8 1.7 33 41-79 3-35 (58)
54 TIGR03879 near_KaiC_dom probab 47.5 2.7 5.8E-05 22.3 -1.4 30 51-80 21-50 (73)
55 PF10668 Phage_terminase: Phag 45.3 8.3 0.00018 19.7 0.3 17 64-80 24-40 (60)
56 PRK07539 NADH dehydrogenase su 44.3 40 0.00087 20.1 3.2 32 48-79 26-57 (154)
57 TIGR01958 nuoE_fam NADH-quinon 44.0 41 0.00089 19.9 3.2 33 47-79 19-51 (148)
58 PRK05988 formate dehydrogenase 43.9 43 0.00092 20.2 3.2 33 47-79 26-58 (156)
59 PF08281 Sigma70_r4_2: Sigma-7 43.7 26 0.00057 16.5 2.0 21 59-79 23-43 (54)
60 cd06171 Sigma70_r4 Sigma70, re 43.0 30 0.00065 15.4 2.1 33 42-79 11-43 (55)
61 PF06971 Put_DNA-bind_N: Putat 42.0 7.9 0.00017 18.9 -0.1 17 64-80 30-46 (50)
62 PF08279 HTH_11: HTH domain; 40.6 17 0.00036 17.3 1.0 16 64-79 17-32 (55)
63 PRK07571 bidirectional hydroge 40.0 52 0.0011 20.1 3.2 31 49-79 41-71 (169)
64 PF13404 HTH_AsnC-type: AsnC-t 39.3 14 0.00029 17.2 0.5 15 65-79 20-34 (42)
65 PF01257 2Fe-2S_thioredx: Thio 38.1 39 0.00085 19.9 2.4 33 47-79 16-48 (145)
66 PF13309 HTH_22: HTH domain 36.6 56 0.0012 16.5 2.6 33 47-79 27-59 (64)
67 TIGR00721 tfx DNA-binding prot 35.9 42 0.00092 19.9 2.3 35 39-79 4-38 (137)
68 PF13730 HTH_36: Helix-turn-he 35.2 21 0.00045 17.0 0.8 19 61-79 24-42 (55)
69 PF00325 Crp: Bacterial regula 34.4 21 0.00045 15.8 0.6 15 64-78 4-18 (32)
70 PRK06759 RNA polymerase factor 32.8 46 0.001 19.0 2.2 17 64-80 124-140 (154)
71 TIGR03209 P21_Cbot clostridium 32.7 77 0.0017 17.9 3.1 17 64-80 125-141 (142)
72 TIGR02959 SigZ RNA polymerase 32.7 47 0.001 19.6 2.2 17 64-80 118-134 (170)
73 PRK12529 RNA polymerase sigma 32.0 51 0.0011 19.7 2.3 17 64-80 145-161 (178)
74 PRK04217 hypothetical protein; 31.9 53 0.0011 18.7 2.2 35 40-79 41-75 (110)
75 PF10078 DUF2316: Uncharacteri 31.9 16 0.00036 20.1 0.1 27 49-79 14-40 (89)
76 cd00569 HTH_Hin_like Helix-tur 31.3 44 0.00096 13.1 3.1 34 41-79 5-38 (42)
77 PF07750 GcrA: GcrA cell cycle 31.1 95 0.0021 18.8 3.3 32 41-77 2-34 (162)
78 PF06056 Terminase_5: Putative 30.6 9.3 0.0002 19.2 -0.9 16 64-79 15-30 (58)
79 PF12793 SgrR_N: Sugar transpo 30.6 40 0.00087 19.2 1.6 33 46-80 5-37 (115)
80 PF05848 CtsR: Firmicute trans 29.6 31 0.00067 20.9 1.0 16 64-79 27-42 (152)
81 PRK10430 DNA-binding transcrip 29.2 49 0.0011 20.5 2.0 39 41-80 158-196 (239)
82 PRK07037 extracytoplasmic-func 29.0 62 0.0013 18.7 2.3 17 64-80 127-143 (163)
83 PF12244 DUF3606: Protein of u 28.9 34 0.00074 17.0 1.0 16 64-79 22-37 (57)
84 PF01325 Fe_dep_repress: Iron 28.3 16 0.00034 18.3 -0.3 32 47-78 7-38 (60)
85 PF13443 HTH_26: Cro/C1-type H 28.2 81 0.0018 15.2 2.6 29 50-78 27-56 (63)
86 smart00421 HTH_LUXR helix_turn 28.2 71 0.0015 14.5 2.1 33 41-79 3-35 (58)
87 TIGR02989 Sig-70_gvs1 RNA poly 27.9 66 0.0014 18.4 2.3 17 63-79 128-144 (159)
88 PRK09648 RNA polymerase sigma 27.8 63 0.0014 19.3 2.2 16 64-79 157-172 (189)
89 PRK09642 RNA polymerase sigma 27.7 67 0.0014 18.5 2.3 17 64-80 124-140 (160)
90 PRK09047 RNA polymerase factor 27.7 67 0.0015 18.4 2.3 17 64-80 124-140 (161)
91 PRK09646 RNA polymerase sigma 27.5 72 0.0016 19.2 2.5 17 64-80 160-176 (194)
92 PF04539 Sigma70_r3: Sigma-70 27.4 28 0.0006 17.8 0.5 16 64-79 22-37 (78)
93 PF01726 LexA_DNA_bind: LexA D 27.4 96 0.0021 15.7 3.3 32 42-75 4-38 (65)
94 TIGR02999 Sig-70_X6 RNA polyme 27.1 67 0.0014 19.0 2.2 17 64-80 152-168 (183)
95 PRK09652 RNA polymerase sigma 27.1 62 0.0013 18.8 2.1 16 64-79 146-161 (182)
96 PRK12526 RNA polymerase sigma 26.3 70 0.0015 19.6 2.2 17 64-80 171-187 (206)
97 PRK15372 pathogenicity island 26.2 53 0.0011 21.8 1.7 31 41-71 11-41 (292)
98 KOG0041|consensus 26.1 1.2E+02 0.0027 19.6 3.3 38 41-78 92-134 (244)
99 PF03444 HrcA_DNA-bdg: Winged 25.7 1.2E+02 0.0026 16.3 2.9 35 43-79 3-40 (78)
100 PRK09645 RNA polymerase sigma 25.4 81 0.0018 18.4 2.4 17 64-80 136-152 (173)
101 PF12802 MarR_2: MarR family; 25.2 50 0.0011 15.8 1.2 35 42-78 3-37 (62)
102 PRK15411 rcsA colanic acid cap 24.7 67 0.0014 19.9 1.9 34 41-80 137-170 (207)
103 TIGR02985 Sig70_bacteroi1 RNA 24.7 80 0.0017 17.9 2.2 17 64-80 131-147 (161)
104 cd08313 Death_TNFR1 Death doma 24.4 40 0.00086 18.1 0.8 14 66-79 15-28 (80)
105 PRK12512 RNA polymerase sigma 24.3 83 0.0018 18.6 2.3 17 64-80 149-165 (184)
106 PRK12537 RNA polymerase sigma 24.2 96 0.0021 18.4 2.5 17 64-80 151-167 (182)
107 PF13412 HTH_24: Winged helix- 24.0 89 0.0019 14.2 2.9 32 44-79 3-34 (48)
108 PRK12515 RNA polymerase sigma 24.0 84 0.0018 18.8 2.3 16 64-79 149-164 (189)
109 COG2197 CitB Response regulato 23.9 87 0.0019 19.5 2.4 35 40-80 147-181 (211)
110 TIGR02954 Sig70_famx3 RNA poly 23.9 86 0.0019 18.3 2.3 17 64-80 137-153 (169)
111 PRK12530 RNA polymerase sigma 23.8 80 0.0017 19.0 2.2 17 64-80 152-168 (189)
112 TIGR02952 Sig70_famx2 RNA poly 23.5 85 0.0018 18.1 2.2 16 64-79 140-155 (170)
113 TIGR02983 SigE-fam_strep RNA p 23.4 80 0.0017 18.2 2.1 17 64-80 128-144 (162)
114 PRK12541 RNA polymerase sigma 23.0 76 0.0016 18.4 1.9 16 64-79 130-145 (161)
115 PF09607 BrkDBD: Brinker DNA-b 22.9 1.1E+02 0.0023 15.5 2.1 14 67-80 30-43 (58)
116 PRK10840 transcriptional regul 22.8 82 0.0018 19.1 2.1 34 41-80 150-183 (216)
117 TIGR01321 TrpR trp operon repr 22.8 1.1E+02 0.0023 17.1 2.3 39 41-79 32-72 (94)
118 PRK11475 DNA-binding transcrip 22.4 79 0.0017 19.7 2.0 34 41-80 134-167 (207)
119 TIGR02937 sigma70-ECF RNA poly 22.3 88 0.0019 17.2 2.0 16 64-79 128-143 (158)
120 PRK09639 RNA polymerase sigma 22.3 91 0.002 18.0 2.1 16 64-79 129-144 (166)
121 PRK00118 putative DNA-binding 22.2 1.1E+02 0.0023 17.3 2.3 33 42-79 18-50 (104)
122 PF15063 TC1: Thyroid cancer p 21.7 98 0.0021 16.6 1.9 32 39-70 31-62 (79)
123 PRK12514 RNA polymerase sigma 21.4 1.2E+02 0.0025 17.9 2.5 17 64-80 147-163 (179)
124 PF12200 DUF3597: Domain of un 21.0 95 0.0021 18.3 1.9 17 60-76 83-99 (127)
125 TIGR00498 lexA SOS regulatory 20.8 1.9E+02 0.0041 17.6 3.4 35 42-78 4-42 (199)
126 PRK00215 LexA repressor; Valid 20.8 77 0.0017 19.4 1.7 35 42-78 2-40 (205)
127 KOG3862|consensus 20.6 38 0.00082 22.7 0.3 26 39-64 223-248 (327)
128 PF13384 HTH_23: Homeodomain-l 20.5 45 0.00098 15.3 0.5 17 63-79 18-34 (50)
129 PRK12543 RNA polymerase sigma 20.1 1.1E+02 0.0024 18.1 2.2 17 64-80 135-151 (179)
No 1
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.42 E-value=5.1e-13 Score=68.15 Aligned_cols=45 Identities=20% Similarity=0.434 Sum_probs=43.4
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHHhCCCccccC
Q psy4349 36 KRMRTSFKHHQLRTMKSYFNINQN----PDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 36 rr~Rt~~t~~ql~~Le~~F~~~~~----p~~~~r~~La~~l~l~~~~Vk 80 (80)
+|.||.||..|+..|+..|+.++| |+...+.+||..|||++.+||
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 689999999999999999999999 999999999999999999886
No 2
>KOG0488|consensus
Probab=99.42 E-value=4.2e-13 Score=88.00 Aligned_cols=51 Identities=24% Similarity=0.401 Sum_probs=48.0
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 30 HSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 30 ~~~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
..++|+|+.||.||..||.+||..|++..|++...|.+||..|||+.+|||
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVK 217 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVK 217 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHH
Confidence 345788889999999999999999999999999999999999999999997
No 3
>KOG0484|consensus
Probab=99.35 E-value=1.8e-13 Score=76.64 Aligned_cols=49 Identities=27% Similarity=0.483 Sum_probs=46.0
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 32 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 32 ~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.++.||.||.||..||.+||+.|...+||++.+|++||.++.|+++.||
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQ 62 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQ 62 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHH
Confidence 4567889999999999999999999999999999999999999998875
No 4
>KOG2251|consensus
Probab=99.34 E-value=1.4e-12 Score=81.37 Aligned_cols=51 Identities=29% Similarity=0.433 Sum_probs=48.2
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 30 HSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 30 ~~~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
..+++.||.||.|+..|+.+||..|.+..||++.+|++||.+|+|++.+||
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVq 82 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQ 82 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhh
Confidence 456788999999999999999999999999999999999999999999886
No 5
>KOG0842|consensus
Probab=99.33 E-value=4.6e-12 Score=82.68 Aligned_cols=50 Identities=16% Similarity=0.293 Sum_probs=47.0
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 31 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 31 ~~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
...++||.|..|+..|..+||+.|..++|++..+|++||..|.|++.|||
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVK 198 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVK 198 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchhee
Confidence 35577888999999999999999999999999999999999999999997
No 6
>KOG0850|consensus
Probab=99.32 E-value=1.6e-12 Score=81.51 Aligned_cols=51 Identities=20% Similarity=0.319 Sum_probs=48.0
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 30 HSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 30 ~~~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+..+|.|++||.|+..||..|.+.|++++|+...+|.+||..|||+..|||
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVK 167 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVK 167 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhh
Confidence 445778889999999999999999999999999999999999999999997
No 7
>KOG0843|consensus
Probab=99.29 E-value=3.3e-12 Score=77.63 Aligned_cols=48 Identities=38% Similarity=0.436 Sum_probs=46.1
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 33 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 33 ~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.+.+|.||.||..||..||..|+.++|....+|+.||+.|+|++.|||
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVk 147 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVK 147 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhh
Confidence 478899999999999999999999999999999999999999999997
No 8
>KOG0489|consensus
Probab=99.27 E-value=2.5e-12 Score=82.75 Aligned_cols=48 Identities=25% Similarity=0.388 Sum_probs=45.9
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 33 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 33 ~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.+.||.||.||..|+.+||+.|+.|+|++...|.+||..|+|+|+|||
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIK 204 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIK 204 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHH
Confidence 457889999999999999999999999999999999999999999997
No 9
>KOG0485|consensus
Probab=99.18 E-value=3.4e-11 Score=75.31 Aligned_cols=49 Identities=22% Similarity=0.355 Sum_probs=46.4
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 32 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 32 ~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
..++||.||+|+..|+..||..|+..+|++..+|..||.+|.|+|.|||
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVK 149 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVK 149 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhh
Confidence 4567889999999999999999999999999999999999999999997
No 10
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.18 E-value=3.1e-11 Score=61.09 Aligned_cols=45 Identities=36% Similarity=0.668 Sum_probs=42.5
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 36 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 36 rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
|+.|+.||..|+..|+..|..++||+...+..||..+||+..+|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 45 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVK 45 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccc
Confidence 568999999999999999999999999999999999999998874
No 11
>KOG0494|consensus
Probab=99.14 E-value=1.6e-10 Score=73.92 Aligned_cols=47 Identities=30% Similarity=0.427 Sum_probs=42.8
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 34 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 34 ~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
++|+-||.||..|+.+||..|...+||+...|+-||.++.|++.+|+
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIq 186 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQ 186 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhh
Confidence 34444999999999999999999999999999999999999998875
No 12
>KOG0487|consensus
Probab=99.09 E-value=2.9e-10 Score=74.42 Aligned_cols=51 Identities=20% Similarity=0.320 Sum_probs=47.6
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 30 HSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 30 ~~~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
...++.||+|.-||..|+.+||+.|..|.|++...|.+|+..|+|+++|||
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVK 280 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVK 280 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhee
Confidence 344677889999999999999999999999999999999999999999997
No 13
>KOG0486|consensus
Probab=99.07 E-value=1.4e-10 Score=75.68 Aligned_cols=48 Identities=27% Similarity=0.472 Sum_probs=45.3
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 33 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 33 ~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+|+||.||.||.+|+.+||..|++|.||+..+|++||..++|++..|+
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvr 157 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 157 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhh
Confidence 477889999999999999999999999999999999999999998874
No 14
>KOG0493|consensus
Probab=99.04 E-value=3.1e-10 Score=72.76 Aligned_cols=45 Identities=33% Similarity=0.490 Sum_probs=43.3
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 36 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 36 rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
||+||.||.+||..|+..|+.|+|+....|.+||+.|+|.+.|||
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIK 291 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIK 291 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhh
Confidence 578999999999999999999999999999999999999999986
No 15
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.04 E-value=4.7e-10 Score=56.33 Aligned_cols=44 Identities=39% Similarity=0.576 Sum_probs=41.4
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 37 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 37 r~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+.|+.|+..|+..|+..|..++||+..++..||..+||+..+|+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVK 45 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 56788999999999999999999999999999999999998874
No 16
>KOG0492|consensus
Probab=99.02 E-value=4.4e-10 Score=69.91 Aligned_cols=50 Identities=18% Similarity=0.319 Sum_probs=46.6
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 31 SHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 31 ~~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
..+..|++||.||..||..||+.|...+|+++.+|.+++..|.|++.|||
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVK 189 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVK 189 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhhee
Confidence 33556889999999999999999999999999999999999999999997
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=1.8e-09 Score=54.58 Aligned_cols=44 Identities=32% Similarity=0.552 Sum_probs=41.4
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 37 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 37 r~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+.|+.|+..++..|+..|..++||+..++..||..+||+..+|+
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~ 45 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVK 45 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHH
Confidence 46789999999999999999999999999999999999998874
No 18
>KOG0491|consensus
Probab=98.86 E-value=2.9e-10 Score=68.49 Aligned_cols=48 Identities=23% Similarity=0.349 Sum_probs=45.0
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 33 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 33 ~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.++++.||+|+..|+..|+..|+..+|++..+|.+||..|+|++.|||
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVK 145 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVK 145 (194)
T ss_pred HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHH
Confidence 345678999999999999999999999999999999999999999986
No 19
>KOG0848|consensus
Probab=98.81 E-value=2.6e-09 Score=68.67 Aligned_cols=47 Identities=21% Similarity=0.360 Sum_probs=44.0
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 34 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 34 ~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.+.+.|.+||..|..+||+.|..++|.++..+.+||..|+|+|+|||
T Consensus 198 TkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVK 244 (317)
T KOG0848|consen 198 TKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVK 244 (317)
T ss_pred cccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhh
Confidence 34467899999999999999999999999999999999999999997
No 20
>KOG0844|consensus
Probab=98.72 E-value=7.5e-09 Score=67.75 Aligned_cols=49 Identities=18% Similarity=0.299 Sum_probs=45.7
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 32 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 32 ~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
...-||.||.||.+|+-.||+.|-+..|.+...|.+||..|+|++..||
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIK 226 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIK 226 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceee
Confidence 3456889999999999999999999999999999999999999999886
No 21
>KOG3802|consensus
Probab=98.64 E-value=2e-08 Score=67.44 Aligned_cols=47 Identities=23% Similarity=0.426 Sum_probs=44.7
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 34 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 34 ~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
|+||+||.|....+..||..|.+|+.|+..+...||.+|+|...+|+
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 67889999999999999999999999999999999999999998874
No 22
>KOG0490|consensus
Probab=98.59 E-value=3.5e-08 Score=61.78 Aligned_cols=49 Identities=18% Similarity=0.059 Sum_probs=45.7
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 32 HQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 32 ~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
..+.++.||.|+..|+.+|++.|+..+||+...++.||..+++++..||
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVq 105 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQ 105 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeee
Confidence 4567889999999999999999999999999999999999999998875
No 23
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.58 E-value=1.3e-07 Score=56.91 Aligned_cols=48 Identities=21% Similarity=0.264 Sum_probs=43.9
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 33 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 33 ~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+..++.|++-|..|+..|+..|+.++||+..+|..|+..++|+++.||
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 445667888999999999999999999999999999999999998876
No 24
>KOG0849|consensus
Probab=98.56 E-value=1e-07 Score=63.85 Aligned_cols=51 Identities=31% Similarity=0.446 Sum_probs=45.5
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 30 HSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 30 ~~~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
...++.+|.||.|+..|+..|+..|++++||++..|+.||.++++++..|+
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riq 221 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQ 221 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHH
Confidence 344556778999999999999999999999999999999999999997763
No 25
>KOG4577|consensus
Probab=98.06 E-value=6e-06 Score=54.05 Aligned_cols=47 Identities=38% Similarity=0.541 Sum_probs=44.3
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 34 RTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 34 ~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
..||+||.+|..||+.|+..|...+.|....|+.|+..+||.-++||
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQ 212 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQ 212 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehh
Confidence 35889999999999999999999999999999999999999998886
No 26
>KOG2252|consensus
Probab=97.89 E-value=1.8e-05 Score=55.39 Aligned_cols=47 Identities=26% Similarity=0.377 Sum_probs=42.9
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 33 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 33 ~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
-..||+|.+||..|...|...|..+++|+..+...|+.+|+|....|
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV 464 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTV 464 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHH
Confidence 34577899999999999999999999999999999999999987655
No 27
>KOG0483|consensus
Probab=97.79 E-value=3.1e-05 Score=48.30 Aligned_cols=44 Identities=18% Similarity=0.348 Sum_probs=40.4
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 37 RMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 37 r~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+++-+|+..|...||..|+.+.++....+..||..|||.++||.
T Consensus 52 ~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVa 95 (198)
T KOG0483|consen 52 GKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVA 95 (198)
T ss_pred cccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHH
Confidence 34458999999999999999999999999999999999999984
No 28
>KOG0847|consensus
Probab=97.42 E-value=8.8e-05 Score=47.02 Aligned_cols=48 Identities=23% Similarity=0.365 Sum_probs=43.4
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 33 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 33 ~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.+++-.|..|+..|+..|+..|+..+|+-...|.+||..+|+++.|||
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvk 212 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVK 212 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHH
Confidence 344556789999999999999999999999999999999999999875
No 29
>KOG1168|consensus
Probab=97.10 E-value=0.00026 Score=46.59 Aligned_cols=46 Identities=30% Similarity=0.578 Sum_probs=42.4
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 35 TKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 35 ~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+||+||.+..-....||..|..++.|+......+|.+|+|-..+|+
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVR 354 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 354 (385)
T ss_pred cccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEE
Confidence 5778999999999999999999999999999999999999887763
No 30
>KOG0774|consensus
Probab=96.91 E-value=0.0012 Score=43.00 Aligned_cols=44 Identities=20% Similarity=0.440 Sum_probs=39.8
Q ss_pred CCCCCcCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 36 KRMRTSFKHHQLRTMKSYFN---INQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 36 rr~Rt~~t~~ql~~Le~~F~---~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
+|+|..|+..-.+.|...|. .|+||+-.++++||.+.+++..||
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQv 235 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQV 235 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhh
Confidence 56788999999999999996 588999999999999999998876
No 31
>KOG0775|consensus
Probab=96.77 E-value=0.0023 Score=41.79 Aligned_cols=38 Identities=24% Similarity=0.495 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 42 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 42 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
|...-...|...|..++||+..++.+||+.+||+..||
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQV 220 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQV 220 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhh
Confidence 34455678999999999999999999999999999887
No 32
>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=96.77 E-value=0.00074 Score=31.84 Aligned_cols=24 Identities=33% Similarity=0.609 Sum_probs=19.3
Q ss_pred hcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 56 INQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 56 ~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
.++||+..++..||..+||+..||
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi 30 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQI 30 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHH
Confidence 479999999999999999999887
No 33
>KOG0490|consensus
Probab=96.64 E-value=0.0028 Score=39.62 Aligned_cols=51 Identities=43% Similarity=0.713 Sum_probs=45.4
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 30 HSHQRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 30 ~~~~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
....+.++.|+.+...|+..+...|..+++|+...+..|+..+++++..|+
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q 198 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQ 198 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhh
Confidence 344567789999999999999999999999999999999999999987653
No 34
>KOG1146|consensus
Probab=95.44 E-value=0.029 Score=43.45 Aligned_cols=48 Identities=27% Similarity=0.462 Sum_probs=43.2
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 33 QRTKRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 33 ~~~rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
..+++.||.++..||..+...|....||...+.+.|...++++.++|+
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~ 948 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQ 948 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhH
Confidence 345778999999999999999999999999999999999999988763
No 35
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=94.11 E-value=0.062 Score=26.80 Aligned_cols=37 Identities=24% Similarity=0.423 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCccc
Q psy4349 42 FKHHQLRTMKSYFNINQN--PDAKDLKQLAQKTGLSKRV 78 (80)
Q Consensus 42 ~t~~ql~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~ 78 (80)
+|..|...|...++...| |-...-.+||..+|++...
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st 39 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKST 39 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHH
Confidence 578899999999998886 6566678999999998753
No 36
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.28 E-value=0.27 Score=24.29 Aligned_cols=39 Identities=18% Similarity=0.301 Sum_probs=28.5
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 36 KRMRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 36 rr~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
+|+|..+|..+...+-..++... ....+|..+|++..+|
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv 39 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTV 39 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHH
Confidence 46788999999998888888776 5678999999998775
No 37
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=89.82 E-value=0.33 Score=30.43 Aligned_cols=38 Identities=26% Similarity=0.456 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCccc
Q psy4349 41 SFKHHQLRTMKSYFNINQN--PDAKDLKQLAQKTGLSKRV 78 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~ 78 (80)
.+|..|+..|...|....| |-...-.+||..+|++...
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 7999999999999999885 6666778999999998753
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=82.30 E-value=0.67 Score=23.38 Aligned_cols=34 Identities=18% Similarity=0.453 Sum_probs=23.7
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 47 LRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 47 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+..|+..|...+++.-.....|..+.+|+..||+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr 43 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVR 43 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHH
Confidence 4569999999999988899999999999988874
No 39
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=74.14 E-value=2.4 Score=19.91 Aligned_cols=35 Identities=9% Similarity=0.312 Sum_probs=15.5
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 40 TSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 40 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
..+|..+...++...... ....++|..+|.+...|
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 357777888887765543 35668999999987654
No 40
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=73.28 E-value=3.3 Score=19.64 Aligned_cols=34 Identities=12% Similarity=0.305 Sum_probs=23.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
.+++.+...+...|..+ ..-.++|..+|++...|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V 37 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTV 37 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHH
Confidence 45677788888777333 35668999999998765
No 41
>KOG0773|consensus
Probab=70.37 E-value=7.7 Score=25.95 Aligned_cols=45 Identities=20% Similarity=0.426 Sum_probs=35.7
Q ss_pred CCCCCCcCCHHHHHHHHHh-hh--hcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 35 TKRMRTSFKHHQLRTMKSY-FN--INQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 35 ~rr~Rt~~t~~ql~~Le~~-F~--~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
..|++..+.......|+.. |+ ..+||....+..||.++||+..||
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv 286 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQV 286 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccC
Confidence 4455568888888888866 33 357999999999999999999886
No 42
>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=69.41 E-value=3.2 Score=20.68 Aligned_cols=32 Identities=28% Similarity=0.434 Sum_probs=21.6
Q ss_pred HHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 45 HQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 45 ~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.|+..|+-.+. +.+.... +||..++++++.|+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHH
Confidence 35666776777 6655444 78999999987653
No 43
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.05 E-value=7.9 Score=21.42 Aligned_cols=37 Identities=11% Similarity=0.024 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccc
Q psy4349 42 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRV 78 (80)
Q Consensus 42 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~ 78 (80)
++..|...-...|+.|--.+....+++|..|+.++-.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~ 39 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVK 39 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHH
Confidence 4566766666666666666667778899999988743
No 44
>PRK13558 bacterio-opsin activator; Provisional
Probab=60.10 E-value=9 Score=27.59 Aligned_cols=39 Identities=18% Similarity=0.326 Sum_probs=33.4
Q ss_pred CcCCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCccc
Q psy4349 40 TSFKHHQLRTMKSYFNINQN--PDAKDLKQLAQKTGLSKRV 78 (80)
Q Consensus 40 t~~t~~ql~~Le~~F~~~~~--p~~~~r~~La~~l~l~~~~ 78 (80)
..+|..|...|+..+....| |=...-.+||..||++...
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t 646 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRST 646 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 47999999999999999987 6666778999999998753
No 45
>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=58.82 E-value=12 Score=17.16 Aligned_cols=15 Identities=20% Similarity=0.370 Sum_probs=12.3
Q ss_pred cCCHHHHHHHHHhhh
Q psy4349 41 SFKHHQLRTMKSYFN 55 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~ 55 (80)
.||..|+..|+.-..
T Consensus 2 ~FT~~Ql~~L~~Qi~ 16 (37)
T PF08880_consen 2 PFTPAQLQELRAQIL 16 (37)
T ss_pred CCCHHHHHHHHHHHH
Confidence 699999999987643
No 46
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=57.84 E-value=12 Score=21.58 Aligned_cols=38 Identities=16% Similarity=0.144 Sum_probs=31.2
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcc
Q psy4349 40 TSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKR 77 (80)
Q Consensus 40 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~ 77 (80)
-.++..-.++|...|...+---...|.++|.++|+.+.
T Consensus 94 yflsesgmeelqdrfmns~st~yrwrke~a~kfgvr~p 131 (143)
T PRK15183 94 YFLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREP 131 (143)
T ss_pred hhhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCC
Confidence 45677778899999988887777889999999998663
No 47
>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=56.88 E-value=25 Score=21.50 Aligned_cols=38 Identities=16% Similarity=0.202 Sum_probs=30.8
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcc
Q psy4349 38 MRTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKR 77 (80)
Q Consensus 38 ~Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~ 77 (80)
....+|.+++.++...-..+ |....+..||.++||+..
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 34689999999988765555 677899999999999864
No 48
>KOG3623|consensus
Probab=56.25 E-value=12 Score=28.38 Aligned_cols=34 Identities=29% Similarity=0.592 Sum_probs=31.1
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 47 LRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 47 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+..|+..|..|..|...+...+|.++||+.+.||
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk 601 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVK 601 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHH
Confidence 6778899999999999999999999999988775
No 49
>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=55.01 E-value=14 Score=17.15 Aligned_cols=34 Identities=15% Similarity=0.408 Sum_probs=20.4
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
.++.++...+...+... ....++|..+|++...|
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~Tv 38 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTV 38 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHH
Confidence 35555555555555555 25668899999987654
No 50
>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=54.57 E-value=22 Score=17.97 Aligned_cols=37 Identities=14% Similarity=0.232 Sum_probs=20.9
Q ss_pred CCCCcCCHHHHHHHHHhh-hhcCCCCHHHHHHHHHHhCCCccc
Q psy4349 37 RMRTSFKHHQLRTMKSYF-NINQNPDAKDLKQLAQKTGLSKRV 78 (80)
Q Consensus 37 r~Rt~~t~~ql~~Le~~F-~~~~~p~~~~r~~La~~l~l~~~~ 78 (80)
+.|..||.++...+-... ... .....+|..+|++..+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~ 39 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPST 39 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeeccccccccc
Confidence 356788888877766555 222 3667889999887654
No 51
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=50.26 E-value=32 Score=21.03 Aligned_cols=36 Identities=6% Similarity=0.050 Sum_probs=29.8
Q ss_pred HHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 44 HHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 44 ~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
..-+..|...+...-|........+|..|+++...|
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 455667787888788999999999999999998655
No 52
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=49.48 E-value=19 Score=21.46 Aligned_cols=34 Identities=12% Similarity=0.180 Sum_probs=25.0
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 40 TSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 40 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
..+++.|...|.. +... ....++|..+|++...|
T Consensus 5 ~~Lt~rqreVL~l-r~~G-----lTq~EIAe~LGiS~~tV 38 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG-----LTQQEIADILGTSRANV 38 (141)
T ss_pred cCCCHHHHHHHHH-HHcC-----CCHHHHHHHHCCCHHHH
Confidence 5678889888876 3322 25678999999998655
No 53
>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=49.12 E-value=16 Score=17.77 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=20.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
.+|..++..|.....-. ...++|..+++++..|
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV 35 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTV 35 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhH
Confidence 56777777776555443 4557788888776544
No 54
>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=47.54 E-value=2.7 Score=22.32 Aligned_cols=30 Identities=10% Similarity=0.275 Sum_probs=20.4
Q ss_pred HHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 51 KSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 51 e~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+..|....|.......++|..+|+++..|+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk 50 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVR 50 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHH
Confidence 334555555455567789999999987653
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=45.30 E-value=8.3 Score=19.67 Aligned_cols=17 Identities=35% Similarity=0.653 Sum_probs=13.4
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.+||..||+++.+|+
T Consensus 24 ~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIR 40 (60)
T ss_pred cHHHHHHHHCCCHHHHH
Confidence 34578999999998773
No 56
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=44.30 E-value=40 Score=20.08 Aligned_cols=32 Identities=9% Similarity=0.048 Sum_probs=23.8
Q ss_pred HHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 48 RTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 48 ~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
..|...=+...|.+......+|..++++..+|
T Consensus 26 ~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v 57 (154)
T PRK07539 26 PALKIVQEQRGWVPDEAIEAVADYLGMPAIDV 57 (154)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 33433334456899999999999999998765
No 57
>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=43.99 E-value=41 Score=19.86 Aligned_cols=33 Identities=6% Similarity=0.040 Sum_probs=24.1
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 47 LRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 47 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
+..|...=+..-|.+......+|..++++...|
T Consensus 19 i~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 19 MPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 334443334455899999999999999998765
No 58
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=43.91 E-value=43 Score=20.17 Aligned_cols=33 Identities=12% Similarity=0.092 Sum_probs=24.6
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 47 LRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 47 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
+..|...=+...|.+......+|..++++..+|
T Consensus 26 i~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V 58 (156)
T PRK05988 26 LPILHAIQDEFGYVPEDAVPVIAEALNLSRAEV 58 (156)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHH
Confidence 344444434556999999999999999998765
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=43.73 E-value=26 Score=16.51 Aligned_cols=21 Identities=14% Similarity=0.232 Sum_probs=12.8
Q ss_pred CCCHHHHHHHHHHhCCCcccc
Q psy4349 59 NPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 59 ~p~~~~r~~La~~l~l~~~~V 79 (80)
|.....-.++|..+|++...|
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v 43 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTV 43 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHH
Confidence 334446778999999988655
No 60
>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=42.99 E-value=30 Score=15.45 Aligned_cols=33 Identities=12% Similarity=0.250 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 42 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 42 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
++..+...+...+..+ .....+|..+|++...|
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i 43 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTV 43 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHH
Confidence 4555666665544322 24567788899887655
No 61
>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=42.02 E-value=7.9 Score=18.92 Aligned_cols=17 Identities=18% Similarity=0.384 Sum_probs=12.0
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.+||..+|++..||+
T Consensus 30 SS~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 30 SSQELAEALGITPAQVR 46 (50)
T ss_dssp -HHHHHHHHTS-HHHHH
T ss_pred CHHHHHHHHCCCHHHhc
Confidence 34578999999998873
No 62
>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=40.64 E-value=17 Score=17.31 Aligned_cols=16 Identities=38% Similarity=0.677 Sum_probs=11.5
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
...+||..++++.+.|
T Consensus 17 t~~eLa~~l~vS~rTi 32 (55)
T PF08279_consen 17 TAKELAEELGVSRRTI 32 (55)
T ss_dssp EHHHHHHHCTS-HHHH
T ss_pred CHHHHHHHhCCCHHHH
Confidence 4557899999988755
No 63
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=39.97 E-value=52 Score=20.15 Aligned_cols=31 Identities=10% Similarity=0.004 Sum_probs=22.9
Q ss_pred HHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 49 TMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 49 ~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
.|...=+..-|.+......+|..+|++...|
T Consensus 41 ~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V 71 (169)
T PRK07571 41 VLHKAQELFGYLERDLLLYVARQLKLPLSRV 71 (169)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHhCcCHHHH
Confidence 3333334456899999999999999998765
No 64
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=39.28 E-value=14 Score=17.20 Aligned_cols=15 Identities=33% Similarity=0.554 Sum_probs=10.9
Q ss_pred HHHHHHHhCCCcccc
Q psy4349 65 LKQLAQKTGLSKRVL 79 (80)
Q Consensus 65 r~~La~~l~l~~~~V 79 (80)
-.+||..+|+++..|
T Consensus 20 ~~~la~~lglS~~~v 34 (42)
T PF13404_consen 20 YAELAEELGLSESTV 34 (42)
T ss_dssp HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHCcCHHHH
Confidence 347899999998765
No 65
>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=38.07 E-value=39 Score=19.88 Aligned_cols=33 Identities=12% Similarity=0.154 Sum_probs=21.6
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 47 LRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 47 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
+..|...=+...|.+......+|..++++..+|
T Consensus 16 l~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v 48 (145)
T PF01257_consen 16 LPILHEVQEEYGYIPEEALEEIAEALGIPPAEV 48 (145)
T ss_dssp HHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHH
Confidence 334444434456899999999999999998765
No 66
>PF13309 HTH_22: HTH domain
Probab=36.63 E-value=56 Score=16.47 Aligned_cols=33 Identities=12% Similarity=0.184 Sum_probs=22.2
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 47 LRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 47 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
+..+...++..-|.-...-..+|..||++...|
T Consensus 27 ~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TV 59 (64)
T PF13309_consen 27 KEIVRQLYEKGIFLLKGAVEYVAEKLGISRATV 59 (64)
T ss_pred HHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHH
Confidence 344444555666666667778999999987543
No 67
>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=35.90 E-value=42 Score=19.89 Aligned_cols=35 Identities=11% Similarity=0.212 Sum_probs=25.2
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 39 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 39 Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
.+.++..|...+... ... ....++|..+|++...|
T Consensus 4 ~~~Lte~qr~VL~Lr-~~G-----lTq~EIAe~LgiS~stV 38 (137)
T TIGR00721 4 KTFLTERQIKVLELR-EKG-----LSQKEIAKELKTTRANV 38 (137)
T ss_pred cCCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCcCHHHH
Confidence 357888898888763 222 25678999999988655
No 68
>PF13730 HTH_36: Helix-turn-helix domain
Probab=35.21 E-value=21 Score=16.96 Aligned_cols=19 Identities=26% Similarity=0.368 Sum_probs=14.1
Q ss_pred CHHHHHHHHHHhCCCcccc
Q psy4349 61 DAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 61 ~~~~r~~La~~l~l~~~~V 79 (80)
+.+....||..+|++...|
T Consensus 24 ~~pS~~~la~~~g~s~~Tv 42 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTV 42 (55)
T ss_pred CCcCHHHHHHHHCcCHHHH
Confidence 4446778899999987655
No 69
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=34.45 E-value=21 Score=15.78 Aligned_cols=15 Identities=20% Similarity=0.403 Sum_probs=10.0
Q ss_pred HHHHHHHHhCCCccc
Q psy4349 64 DLKQLAQKTGLSKRV 78 (80)
Q Consensus 64 ~r~~La~~l~l~~~~ 78 (80)
.+.++|..+|++...
T Consensus 4 tr~diA~~lG~t~ET 18 (32)
T PF00325_consen 4 TRQDIADYLGLTRET 18 (32)
T ss_dssp -HHHHHHHHTS-HHH
T ss_pred CHHHHHHHhCCcHHH
Confidence 467889999887643
No 70
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=32.78 E-value=46 Score=19.02 Aligned_cols=17 Identities=12% Similarity=0.239 Sum_probs=13.2
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
...++|..+|++...|+
T Consensus 124 s~~EIA~~l~is~~tV~ 140 (154)
T PRK06759 124 TMGEIALETEMTYYQVR 140 (154)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999987663
No 71
>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=32.71 E-value=77 Score=17.94 Aligned_cols=17 Identities=18% Similarity=0.237 Sum_probs=13.1
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|++...|+
T Consensus 125 s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 125 KEIDIAKKLHISRQSVY 141 (142)
T ss_pred CHHHHHHHHCcCHHhhc
Confidence 34588999999987764
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=32.69 E-value=47 Score=19.61 Aligned_cols=17 Identities=29% Similarity=0.362 Sum_probs=12.5
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
...++|..+|++...|+
T Consensus 118 s~~eIA~~lgis~~tV~ 134 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAK 134 (170)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45578889998886653
No 73
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=31.95 E-value=51 Score=19.65 Aligned_cols=17 Identities=18% Similarity=0.266 Sum_probs=12.9
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|+++..|+
T Consensus 145 s~~EIA~~lgis~~tVk 161 (178)
T PRK12529 145 KQKDIAQALDIALPTVK 161 (178)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45588999999887653
No 74
>PRK04217 hypothetical protein; Provisional
Probab=31.94 E-value=53 Score=18.71 Aligned_cols=35 Identities=6% Similarity=0.116 Sum_probs=24.3
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 40 TSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 40 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
..++..+...+...+.... ...++|..+|++...|
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV 75 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTV 75 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHH
Confidence 4677888777765554332 5567899999988655
No 75
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=31.86 E-value=16 Score=20.10 Aligned_cols=27 Identities=26% Similarity=0.413 Sum_probs=16.7
Q ss_pred HHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 49 TMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 49 ~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
+|...|....+ ..+.+|..|+++...|
T Consensus 14 ELq~nf~~~~l----s~~~ia~dL~~s~~~l 40 (89)
T PF10078_consen 14 ELQANFELSGL----SLEQIAADLGTSPEHL 40 (89)
T ss_pred HHHHHHHHcCC----CHHHHHHHhCCCHHHH
Confidence 45555665554 4556788888776543
No 76
>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=31.31 E-value=44 Score=13.10 Aligned_cols=34 Identities=15% Similarity=0.394 Sum_probs=19.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
.++..+...+...+... + ....+|..++++...|
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv 38 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTL 38 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHH
Confidence 34556555555555432 2 4457788888876543
No 77
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=31.13 E-value=95 Score=18.83 Aligned_cols=32 Identities=16% Similarity=0.395 Sum_probs=22.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhC-CCcc
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTG-LSKR 77 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~-l~~~ 77 (80)
.+|.+.+..|...+.... .-.++|.+|| ++..
T Consensus 2 ~Wtde~~~~L~~lw~~G~-----SasqIA~~lg~vsRn 34 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL-----SASQIARQLGGVSRN 34 (162)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCcchh
Confidence 467888888888776553 4557788888 6654
No 78
>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=30.63 E-value=9.3 Score=19.16 Aligned_cols=16 Identities=19% Similarity=0.586 Sum_probs=12.6
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
...++|..||++...|
T Consensus 15 ~~~eIA~~Lg~~~~TV 30 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTV 30 (58)
T ss_pred CHHHHHHHHCCChHHH
Confidence 4568899999987655
No 79
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=30.62 E-value=40 Score=19.21 Aligned_cols=33 Identities=21% Similarity=0.218 Sum_probs=21.4
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 46 QLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 46 ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
+...|...|. .-+......+||..+.++.+.++
T Consensus 5 ~y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r 37 (115)
T PF12793_consen 5 QYQRLWQHYG--GQPVEVTLDELAELLFCSRRNAR 37 (115)
T ss_pred HHHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHH
Confidence 4445555555 23444566789999999987653
No 80
>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=29.57 E-value=31 Score=20.93 Aligned_cols=16 Identities=13% Similarity=0.173 Sum_probs=12.5
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
.|.+||.+++|-+.||
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 6789999999999886
No 81
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=29.22 E-value=49 Score=20.52 Aligned_cols=39 Identities=15% Similarity=0.248 Sum_probs=26.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.+|..++..+......+ +-....-.++|..+++++..|+
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~ 196 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCR 196 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHH
Confidence 46777776665544433 4444566789999999988764
No 82
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.97 E-value=62 Score=18.72 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=12.8
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
...++|..+|++...|+
T Consensus 127 s~~EIA~~lgis~~tV~ 143 (163)
T PRK07037 127 TQKDIARELGVSPTLVN 143 (163)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45588999999887653
No 83
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=28.88 E-value=34 Score=17.00 Aligned_cols=16 Identities=19% Similarity=0.484 Sum_probs=10.4
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
+...+|..+|+++.++
T Consensus 22 ev~ywa~~~gvt~~~L 37 (57)
T PF12244_consen 22 EVRYWAKRFGVTEEQL 37 (57)
T ss_pred HHHHHHHHHCcCHHHH
Confidence 4456677777776654
No 84
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=28.29 E-value=16 Score=18.32 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=17.8
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCccc
Q psy4349 47 LRTMKSYFNINQNPDAKDLKQLAQKTGLSKRV 78 (80)
Q Consensus 47 l~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~ 78 (80)
-..|+..|....--.......||..++++...
T Consensus 7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~t 38 (60)
T PF01325_consen 7 EDYLKAIYELSEEGGPVRTKDIAERLGVSPPT 38 (60)
T ss_dssp HHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHcCCCCccHHHHHHHHCCChHH
Confidence 34555565544322223445789999888754
No 85
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=28.23 E-value=81 Score=15.16 Aligned_cols=29 Identities=21% Similarity=0.303 Sum_probs=15.5
Q ss_pred HHHhhhhc-CCCCHHHHHHHHHHhCCCccc
Q psy4349 50 MKSYFNIN-QNPDAKDLKQLAQKTGLSKRV 78 (80)
Q Consensus 50 Le~~F~~~-~~p~~~~r~~La~~l~l~~~~ 78 (80)
+...+... ..+.......||..|+++...
T Consensus 27 l~~~~~~~~~~~~~~~l~~ia~~l~~~~~e 56 (63)
T PF13443_consen 27 LSRILNGKPSNPSLDTLEKIAKALNCSPEE 56 (63)
T ss_dssp HHHHHTTT-----HHHHHHHHHHHT--HHH
T ss_pred HHHHHhcccccccHHHHHHHHHHcCCCHHH
Confidence 33344444 468888888899999887643
No 86
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=28.16 E-value=71 Score=14.47 Aligned_cols=33 Identities=15% Similarity=0.283 Sum_probs=20.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
.++..+...+...+ .. ....++|..++++...|
T Consensus 3 ~l~~~e~~i~~~~~-~g-----~s~~eia~~l~is~~tv 35 (58)
T smart00421 3 SLTPREREVLRLLA-EG-----LTNKEIAERLGISEKTV 35 (58)
T ss_pred CCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHH
Confidence 35666666665432 22 14467888899887654
No 87
>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=27.89 E-value=66 Score=18.42 Aligned_cols=17 Identities=24% Similarity=0.343 Sum_probs=12.9
Q ss_pred HHHHHHHHHhCCCcccc
Q psy4349 63 KDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 63 ~~r~~La~~l~l~~~~V 79 (80)
..-.++|..+|++...|
T Consensus 128 ~~~~eIA~~l~is~~tv 144 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAV 144 (159)
T ss_pred CCHHHHHHHhCCCHHHH
Confidence 35568899999988765
No 88
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=27.76 E-value=63 Score=19.31 Aligned_cols=16 Identities=13% Similarity=0.229 Sum_probs=12.6
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
.-.++|..+|++...|
T Consensus 157 s~~EIA~~lgis~~tV 172 (189)
T PRK09648 157 SAEETAEAVGSTPGAV 172 (189)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4568899999988765
No 89
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=27.75 E-value=67 Score=18.54 Aligned_cols=17 Identities=6% Similarity=0.298 Sum_probs=12.5
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|++...|+
T Consensus 124 s~~EIA~~lgis~~tV~ 140 (160)
T PRK09642 124 SYQEIALQEKIEVKTVE 140 (160)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 34478999999887663
No 90
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=27.71 E-value=67 Score=18.43 Aligned_cols=17 Identities=24% Similarity=0.345 Sum_probs=12.7
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|++...|+
T Consensus 124 s~~EIA~~lgis~~tV~ 140 (161)
T PRK09047 124 DVAETAAAMGCSEGSVK 140 (161)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 34588999999887653
No 91
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=27.55 E-value=72 Score=19.23 Aligned_cols=17 Identities=6% Similarity=0.288 Sum_probs=12.8
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|++...|+
T Consensus 160 s~~EIA~~Lgis~~tVk 176 (194)
T PRK09646 160 TYREVAERLAVPLGTVK 176 (194)
T ss_pred CHHHHHHHhCCChHhHH
Confidence 45578999999887664
No 92
>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=27.44 E-value=28 Score=17.80 Aligned_cols=16 Identities=19% Similarity=0.333 Sum_probs=11.7
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
...+||..+|++...|
T Consensus 22 t~eEiA~~lgis~~~v 37 (78)
T PF04539_consen 22 TDEEIAEELGISVEEV 37 (78)
T ss_dssp BHHHHHHHHTS-HHHH
T ss_pred CHHHHHHHHcccHHHH
Confidence 5668899999987654
No 93
>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=27.41 E-value=96 Score=15.73 Aligned_cols=32 Identities=19% Similarity=0.358 Sum_probs=19.2
Q ss_pred CCHHHHHHHHHh---hhhcCCCCHHHHHHHHHHhCCC
Q psy4349 42 FKHHQLRTMKSY---FNINQNPDAKDLKQLAQKTGLS 75 (80)
Q Consensus 42 ~t~~ql~~Le~~---F~~~~~p~~~~r~~La~~l~l~ 75 (80)
+|..|...|+-. ...+-||. ...+||..+|+.
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 566676666543 45666773 556899999987
No 94
>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=27.14 E-value=67 Score=18.97 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=12.7
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|+++..|+
T Consensus 152 s~~EIA~~lgis~~tVk 168 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVE 168 (183)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 44578999999887664
No 95
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=27.07 E-value=62 Score=18.82 Aligned_cols=16 Identities=13% Similarity=0.247 Sum_probs=12.2
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
.-.++|..+|++...|
T Consensus 146 s~~eIA~~lgis~~tV 161 (182)
T PRK09652 146 SYEEIAEIMGCPIGTV 161 (182)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4457899999988765
No 96
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=26.34 E-value=70 Score=19.60 Aligned_cols=17 Identities=24% Similarity=0.294 Sum_probs=13.0
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
...++|..+|++...|+
T Consensus 171 s~~EIA~~lgis~~tV~ 187 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVK 187 (206)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45688999999887663
No 97
>PRK15372 pathogenicity island 2 effector protein SseI; Provisional
Probab=26.16 E-value=53 Score=21.80 Aligned_cols=31 Identities=13% Similarity=0.294 Sum_probs=25.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHH
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQK 71 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~ 71 (80)
.++.+|-+.|+..|..+|.|....+++++..
T Consensus 11 FcsTHq~EAl~CI~~LcHP~~gtTpe~I~s~ 41 (292)
T PRK15372 11 FCSTHQTEALECIWTICHPPAGTTREDVVSR 41 (292)
T ss_pred hccccHHHHHHHHHHHhCCCCCCCHHHHHHH
Confidence 4677899999999999999877777776554
No 98
>KOG0041|consensus
Probab=26.14 E-value=1.2e+02 Score=19.60 Aligned_cols=38 Identities=24% Similarity=0.391 Sum_probs=31.0
Q ss_pred cCCHHHHHHHHHhhh-----hcCCCCHHHHHHHHHHhCCCccc
Q psy4349 41 SFKHHQLRTMKSYFN-----INQNPDAKDLKQLAQKTGLSKRV 78 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~-----~~~~p~~~~r~~La~~l~l~~~~ 78 (80)
-|+..|+..++.+|. +.-|.+.-+...+..+||.+...
T Consensus 92 eFsrkqIk~~~~~Fk~yDe~rDgfIdl~ELK~mmEKLgapQTH 134 (244)
T KOG0041|consen 92 EFSRKQIKDAESMFKQYDEDRDGFIDLMELKRMMEKLGAPQTH 134 (244)
T ss_pred HHHHHHHHHHHHHHHHhcccccccccHHHHHHHHHHhCCchhh
Confidence 577889999999984 46699999999999999987653
No 99
>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=25.72 E-value=1.2e+02 Score=16.28 Aligned_cols=35 Identities=20% Similarity=0.306 Sum_probs=18.4
Q ss_pred CHHHHHHHHHh---hhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 43 KHHQLRTMKSY---FNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 43 t~~ql~~Le~~---F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
|..|...|... |....-|... ..||..++++.+.|
T Consensus 3 t~rq~~IL~alV~~Y~~~~~PVgS--k~ia~~l~~s~aTI 40 (78)
T PF03444_consen 3 TERQREILKALVELYIETGEPVGS--KTIAEELGRSPATI 40 (78)
T ss_pred CHHHHHHHHHHHHHHHhcCCCcCH--HHHHHHHCCChHHH
Confidence 44555555444 4444444332 25666777776554
No 100
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.41 E-value=81 Score=18.43 Aligned_cols=17 Identities=18% Similarity=0.374 Sum_probs=12.6
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|+++..|+
T Consensus 136 s~~EIA~~lgis~~tV~ 152 (173)
T PRK09645 136 STAQIAADLGIPEGTVK 152 (173)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 34588999999887653
No 101
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=25.22 E-value=50 Score=15.78 Aligned_cols=35 Identities=20% Similarity=0.284 Sum_probs=21.0
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccc
Q psy4349 42 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRV 78 (80)
Q Consensus 42 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~ 78 (80)
++..|...|........- .....+||..++++...
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~ 37 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKST 37 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHH
Confidence 567777777655554432 12455788888887643
No 102
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=24.72 E-value=67 Score=19.86 Aligned_cols=34 Identities=6% Similarity=0.216 Sum_probs=24.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.+|+.+++.|.-.-+-. ...++|.++++++..|+
T Consensus 137 ~LT~RE~eVL~lla~G~------snkeIA~~L~iS~~TVk 170 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQ------GTIQISDQMNIKAKTVS 170 (207)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHcCCCHHHHH
Confidence 48888888886443322 45688999999987764
No 103
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=24.72 E-value=80 Score=17.86 Aligned_cols=17 Identities=24% Similarity=0.556 Sum_probs=12.6
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
...++|..+|+++..|+
T Consensus 131 ~~~eIA~~lgis~~tv~ 147 (161)
T TIGR02985 131 SYKEIAEELGISVKTVE 147 (161)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45578899999887653
No 104
>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=24.44 E-value=40 Score=18.06 Aligned_cols=14 Identities=29% Similarity=0.582 Sum_probs=11.5
Q ss_pred HHHHHHhCCCcccc
Q psy4349 66 KQLAQKTGLSKRVL 79 (80)
Q Consensus 66 ~~La~~l~l~~~~V 79 (80)
..+|..+||++.+|
T Consensus 15 k~~~R~LGlse~~I 28 (80)
T cd08313 15 KEFVRRLGLSDNEI 28 (80)
T ss_pred HHHHHHcCCCHHHH
Confidence 46899999998765
No 105
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=24.27 E-value=83 Score=18.65 Aligned_cols=17 Identities=24% Similarity=0.393 Sum_probs=12.8
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|++...|+
T Consensus 149 s~~eIA~~l~is~~tV~ 165 (184)
T PRK12512 149 SIKETAAKLSMSEGAVR 165 (184)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 45588999999887653
No 106
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=24.24 E-value=96 Score=18.44 Aligned_cols=17 Identities=18% Similarity=0.300 Sum_probs=12.9
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|++...|+
T Consensus 151 s~~eIA~~lgis~~tV~ 167 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVK 167 (182)
T ss_pred CHHHHHHHHCCChhhHH
Confidence 44578999999887663
No 107
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=24.04 E-value=89 Score=14.23 Aligned_cols=32 Identities=25% Similarity=0.346 Sum_probs=17.8
Q ss_pred HHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 44 HHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 44 ~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
..+...|....+ ++. ....+||..+|++...|
T Consensus 3 ~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv 34 (48)
T PF13412_consen 3 ETQRKILNYLRE-NPR---ITQKELAEKLGISRSTV 34 (48)
T ss_dssp HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHH
Confidence 344555544444 433 35668899999987543
No 108
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=23.96 E-value=84 Score=18.79 Aligned_cols=16 Identities=6% Similarity=0.412 Sum_probs=11.9
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
.-.++|..+|++...|
T Consensus 149 s~~eIA~~lgis~~tV 164 (189)
T PRK12515 149 SVEEVGEIVGIPESTV 164 (189)
T ss_pred CHHHHHHHHCcCHHHH
Confidence 4457888899888665
No 109
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=23.95 E-value=87 Score=19.50 Aligned_cols=35 Identities=14% Similarity=0.229 Sum_probs=24.7
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 40 TSFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 40 t~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
..+|+.+...|...-+- ..-.++|.+|++++..||
T Consensus 147 ~~LT~RE~eVL~lla~G------~snkeIA~~L~iS~~TVk 181 (211)
T COG2197 147 ELLTPRELEVLRLLAEG------LSNKEIAEELNLSEKTVK 181 (211)
T ss_pred CCCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHhHHH
Confidence 46888888887643222 244588999999998775
No 110
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=23.91 E-value=86 Score=18.29 Aligned_cols=17 Identities=12% Similarity=0.286 Sum_probs=12.8
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
...++|..+|++...|+
T Consensus 137 s~~eiA~~lgis~~tv~ 153 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVK 153 (169)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 44588999999887653
No 111
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=23.79 E-value=80 Score=19.01 Aligned_cols=17 Identities=24% Similarity=0.335 Sum_probs=13.0
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|+++..|+
T Consensus 152 s~~EIA~~lgis~~tVk 168 (189)
T PRK12530 152 SSEQICQECDISTSNLH 168 (189)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 45588999999987664
No 112
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=23.53 E-value=85 Score=18.14 Aligned_cols=16 Identities=13% Similarity=0.289 Sum_probs=12.0
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
.-.++|..+|++...|
T Consensus 140 s~~eIA~~l~is~~tv 155 (170)
T TIGR02952 140 PIAEVARILGKTEGAV 155 (170)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4457888899887665
No 113
>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=23.36 E-value=80 Score=18.19 Aligned_cols=17 Identities=24% Similarity=0.323 Sum_probs=12.9
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|++...|+
T Consensus 128 s~~eIA~~lgis~~tV~ 144 (162)
T TIGR02983 128 SEAQVAEALGISVGTVK 144 (162)
T ss_pred CHHHHHHHhCCCHHHHH
Confidence 44578999999987664
No 114
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=22.99 E-value=76 Score=18.35 Aligned_cols=16 Identities=38% Similarity=0.492 Sum_probs=11.8
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
.-.++|..+|++...|
T Consensus 130 s~~eIA~~lgis~~tv 145 (161)
T PRK12541 130 SYKEIAEMTGLSLAKV 145 (161)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4457888888887665
No 115
>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=22.89 E-value=1.1e+02 Score=15.52 Aligned_cols=14 Identities=29% Similarity=0.408 Sum_probs=9.3
Q ss_pred HHHHHhCCCccccC
Q psy4349 67 QLAQKTGLSKRVLQ 80 (80)
Q Consensus 67 ~La~~l~l~~~~Vk 80 (80)
..|.++|+++.+|+
T Consensus 30 Aaarkf~V~r~~Vr 43 (58)
T PF09607_consen 30 AAARKFNVSRRQVR 43 (58)
T ss_dssp HHHHHTTS-HHHHH
T ss_pred HHHHHhCccHHHHH
Confidence 34888888887663
No 116
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=22.83 E-value=82 Score=19.06 Aligned_cols=34 Identities=9% Similarity=0.129 Sum_probs=23.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.+|+.+.+.|....+- ..-.++|..+++++..|+
T Consensus 150 ~Lt~rE~evl~~~~~G------~s~~eIA~~l~iS~~TV~ 183 (216)
T PRK10840 150 RLSPKESEVLRLFAEG------FLVTEIAKKLNRSIKTIS 183 (216)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHH
Confidence 4788888887665433 245578899988887663
No 117
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=22.78 E-value=1.1e+02 Score=17.09 Aligned_cols=39 Identities=13% Similarity=0.199 Sum_probs=23.5
Q ss_pred cCCHHHHHHHHHhhhhcCCC--CHHHHHHHHHHhCCCcccc
Q psy4349 41 SFKHHQLRTMKSYFNINQNP--DAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p--~~~~r~~La~~l~l~~~~V 79 (80)
.+|+..+..+...+..-..+ ......++|..+|++.+.|
T Consensus 32 lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atI 72 (94)
T TIGR01321 32 ILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATI 72 (94)
T ss_pred hCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhh
Confidence 46667777777665544311 1123457888888887654
No 118
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=22.43 E-value=79 Score=19.69 Aligned_cols=34 Identities=6% Similarity=0.081 Sum_probs=23.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccccC
Q psy4349 41 SFKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 41 ~~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~Vk 80 (80)
.+|+.+.+.|....+-. .-.++|..|++++..|+
T Consensus 134 ~LT~RE~eVL~ll~~G~------snkeIA~~L~iS~~TV~ 167 (207)
T PRK11475 134 MLSPTEREILRFMSRGY------SMPQIAEQLERNIKTIR 167 (207)
T ss_pred CCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHH
Confidence 47888888876554432 45578888988887663
No 119
>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=22.33 E-value=88 Score=17.18 Aligned_cols=16 Identities=25% Similarity=0.409 Sum_probs=12.2
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
...++|..+|+++..|
T Consensus 128 s~~eIA~~l~~s~~~v 143 (158)
T TIGR02937 128 SYKEIAEILGISVGTV 143 (158)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4558899999987655
No 120
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=22.32 E-value=91 Score=18.01 Aligned_cols=16 Identities=19% Similarity=0.457 Sum_probs=12.3
Q ss_pred HHHHHHHHhCCCcccc
Q psy4349 64 DLKQLAQKTGLSKRVL 79 (80)
Q Consensus 64 ~r~~La~~l~l~~~~V 79 (80)
.-.++|..+|++...|
T Consensus 129 s~~eIA~~lgis~~tV 144 (166)
T PRK09639 129 SYKEIAEALGIKESSV 144 (166)
T ss_pred CHHHHHHHHCCCHHHH
Confidence 4567888899888765
No 121
>PRK00118 putative DNA-binding protein; Validated
Probab=22.23 E-value=1.1e+02 Score=17.31 Aligned_cols=33 Identities=18% Similarity=0.340 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccc
Q psy4349 42 FKHHQLRTMKSYFNINQNPDAKDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 42 ~t~~ql~~Le~~F~~~~~p~~~~r~~La~~l~l~~~~V 79 (80)
++..|...+...|.... ...++|..+|++...|
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV 50 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAV 50 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHH
Confidence 34555555544433332 4557899999887654
No 122
>PF15063 TC1: Thyroid cancer protein 1
Probab=21.69 E-value=98 Score=16.63 Aligned_cols=32 Identities=13% Similarity=0.273 Sum_probs=25.6
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHH
Q psy4349 39 RTSFKHHQLRTMKSYFNINQNPDAKDLKQLAQ 70 (80)
Q Consensus 39 Rt~~t~~ql~~Le~~F~~~~~p~~~~r~~La~ 70 (80)
--.|....+..|.+.|+..--....+|..+--
T Consensus 31 aNIFe~vn~~qlqrLF~~sGD~kAEeRA~iI~ 62 (79)
T PF15063_consen 31 ANIFENVNLDQLQRLFQKSGDKKAEERARIIW 62 (79)
T ss_pred hhhhhccCHHHHHHHHHHccchhHHHHHHHHH
Confidence 34788888889999999998888888876543
No 123
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.37 E-value=1.2e+02 Score=17.89 Aligned_cols=17 Identities=18% Similarity=0.407 Sum_probs=13.2
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
...++|..+|+++..|+
T Consensus 147 s~~eIA~~lgis~~tV~ 163 (179)
T PRK12514 147 SYKELAERHDVPLNTMR 163 (179)
T ss_pred CHHHHHHHHCCChHHHH
Confidence 45688999999987663
No 124
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=21.00 E-value=95 Score=18.30 Aligned_cols=17 Identities=24% Similarity=0.325 Sum_probs=11.7
Q ss_pred CCHHHHHHHHHHhCCCc
Q psy4349 60 PDAKDLKQLAQKTGLSK 76 (80)
Q Consensus 60 p~~~~r~~La~~l~l~~ 76 (80)
.+...|.+||..|+++.
T Consensus 83 SSl~aRkeLA~eL~~~~ 99 (127)
T PF12200_consen 83 SSLAARKELAKELGYTG 99 (127)
T ss_dssp -SHHHHHHHHHHHT---
T ss_pred CCHHHHHHHHHHhCCCC
Confidence 56789999999999864
No 125
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=20.78 E-value=1.9e+02 Score=17.56 Aligned_cols=35 Identities=14% Similarity=0.274 Sum_probs=23.6
Q ss_pred CCHHHHHHHHHhh---hhcCCCCHHHHHHHHHHhCCC-ccc
Q psy4349 42 FKHHQLRTMKSYF---NINQNPDAKDLKQLAQKTGLS-KRV 78 (80)
Q Consensus 42 ~t~~ql~~Le~~F---~~~~~p~~~~r~~La~~l~l~-~~~ 78 (80)
+|..|...|+... ..+.++ ....+||..++++ ...
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~--~~~~ela~~~~~~s~~t 42 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYP--PSIREIARAVGLRSPSA 42 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCC--CcHHHHHHHhCCCChHH
Confidence 5677777777665 345555 3355899999997 543
No 126
>PRK00215 LexA repressor; Validated
Probab=20.76 E-value=77 Score=19.41 Aligned_cols=35 Identities=17% Similarity=0.236 Sum_probs=22.5
Q ss_pred CCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHhCC-Cccc
Q psy4349 42 FKHHQLRTMKSYFN---INQNPDAKDLKQLAQKTGL-SKRV 78 (80)
Q Consensus 42 ~t~~ql~~Le~~F~---~~~~p~~~~r~~La~~l~l-~~~~ 78 (80)
+|..|...|+...+ .+.++ ....+||..+|+ +...
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~t 40 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSA 40 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHH
Confidence 46778888776653 33333 245588999998 6543
No 127
>KOG3862|consensus
Probab=20.61 E-value=38 Score=22.74 Aligned_cols=26 Identities=15% Similarity=0.291 Sum_probs=22.2
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHH
Q psy4349 39 RTSFKHHQLRTMKSYFNINQNPDAKD 64 (80)
Q Consensus 39 Rt~~t~~ql~~Le~~F~~~~~p~~~~ 64 (80)
-..|+..+++.|...|++.+|+....
T Consensus 223 ~d~ft~~~~~~ld~~~~r~~y~~~~~ 248 (327)
T KOG3862|consen 223 ADAFTQQHLEPLDRSFERPHYPLVYA 248 (327)
T ss_pred cccccccccccccceeeccccccccc
Confidence 34899999999999999999987653
No 128
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.49 E-value=45 Score=15.35 Aligned_cols=17 Identities=18% Similarity=0.534 Sum_probs=11.1
Q ss_pred HHHHHHHHHhCCCcccc
Q psy4349 63 KDLKQLAQKTGLSKRVL 79 (80)
Q Consensus 63 ~~r~~La~~l~l~~~~V 79 (80)
....++|..+|++...|
T Consensus 18 ~s~~~ia~~lgvs~~Tv 34 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTV 34 (50)
T ss_dssp --HHHHHHHHTS-HHHH
T ss_pred CCHHHHHHHHCcCHHHH
Confidence 35668899999987654
No 129
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=20.10 E-value=1.1e+02 Score=18.11 Aligned_cols=17 Identities=12% Similarity=0.173 Sum_probs=12.5
Q ss_pred HHHHHHHHhCCCccccC
Q psy4349 64 DLKQLAQKTGLSKRVLQ 80 (80)
Q Consensus 64 ~r~~La~~l~l~~~~Vk 80 (80)
.-.++|..+|++...|+
T Consensus 135 s~~EIA~~lgis~~tV~ 151 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVK 151 (179)
T ss_pred CHHHHHHHHCCCHHHHH
Confidence 44578999999886653
Done!