Query psy7603
Match_columns 130
No_of_seqs 103 out of 340
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 22:36:09 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7603.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7603hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1815|consensus 98.9 1.3E-09 2.8E-14 93.6 6.3 77 46-123 2-81 (444)
2 PF14555 UBA_4: UBA-like domai 98.0 1.2E-05 2.5E-10 48.3 4.9 40 57-97 1-40 (43)
3 PF00627 UBA: UBA/TS-N domain; 92.7 0.4 8.7E-06 27.3 4.7 33 57-90 3-35 (37)
4 smart00804 TAP_C C-terminal do 92.6 0.66 1.4E-05 30.1 6.0 42 53-94 9-50 (63)
5 PF03943 TAP_C: TAP C-terminal 92.1 0.11 2.4E-06 32.3 1.9 38 57-94 1-38 (51)
6 cd00194 UBA Ubiquitin Associat 91.5 0.78 1.7E-05 25.9 5.0 35 58-93 3-37 (38)
7 smart00165 UBA Ubiquitin assoc 89.4 1.4 3E-05 24.7 4.7 33 59-92 4-36 (37)
8 PF02845 CUE: CUE domain; Int 86.6 2.7 5.9E-05 24.5 4.9 37 58-94 3-40 (42)
9 smart00546 CUE Domain that may 81.0 7.3 0.00016 22.6 5.2 38 57-94 3-41 (43)
10 KOG3154|consensus 77.6 3.3 7.1E-05 33.7 3.7 31 70-100 162-199 (263)
11 PF06056 Terminase_5: Putative 75.3 3.9 8.4E-05 25.9 2.9 31 59-89 15-45 (58)
12 PF08667 BetR: BetR domain; I 67.8 15 0.00034 27.7 5.1 66 58-123 23-94 (147)
13 PF13384 HTH_23: Homeodomain-l 65.1 7.4 0.00016 22.8 2.5 26 57-82 17-42 (50)
14 PF02042 RWP-RK: RWP-RK domain 64.6 10 0.00023 23.7 3.1 37 46-82 4-40 (52)
15 PF04034 DUF367: Domain of unk 63.7 13 0.00029 27.4 4.0 53 40-101 60-119 (127)
16 PF10245 MRP-S22: Mitochondria 62.5 10 0.00022 31.0 3.4 33 39-71 32-64 (243)
17 PRK04217 hypothetical protein; 62.4 28 0.0006 24.9 5.4 52 40-94 36-92 (110)
18 PF05138 PaaA_PaaC: Phenylacet 60.0 13 0.00029 30.1 3.8 61 49-110 167-227 (263)
19 PF12728 HTH_17: Helix-turn-he 57.6 13 0.00028 21.9 2.6 21 60-80 4-24 (51)
20 PF15586 Imm47: Immunity prote 56.7 22 0.00049 25.5 4.1 40 17-58 20-61 (116)
21 PF04703 FaeA: FaeA-like prote 55.1 17 0.00037 23.4 3.0 31 50-80 3-38 (62)
22 PRK11426 hypothetical protein; 53.1 23 0.00049 26.3 3.7 38 44-81 58-96 (132)
23 PF02954 HTH_8: Bacterial regu 50.4 24 0.00052 20.4 2.9 23 59-81 20-42 (42)
24 TIGR01764 excise DNA binding d 50.3 22 0.00047 19.9 2.7 21 60-80 4-24 (49)
25 PF13518 HTH_28: Helix-turn-he 49.3 16 0.00035 21.2 2.0 24 59-82 14-37 (52)
26 TIGR03595 Obg_CgtA_exten Obg f 48.5 45 0.00097 21.6 4.3 47 73-119 17-67 (69)
27 PF00325 Crp: Bacterial regula 48.1 15 0.00033 20.7 1.7 21 61-81 6-26 (32)
28 PRK09624 porD pyuvate ferredox 47.7 12 0.00026 26.1 1.5 15 80-94 5-19 (105)
29 PF12668 DUF3791: Protein of u 47.5 40 0.00087 21.1 3.8 27 56-82 4-30 (62)
30 PRK02287 hypothetical protein; 46.7 34 0.00075 26.4 4.0 38 63-101 116-160 (171)
31 PRK09377 tsf elongation factor 45.4 85 0.0019 26.1 6.4 60 58-117 7-66 (290)
32 TIGR02158 PA_CoA_Oxy3 phenylac 45.4 1.1E+02 0.0023 24.7 6.8 62 50-112 142-203 (237)
33 PHA00675 hypothetical protein 45.3 82 0.0018 21.4 5.2 55 31-85 7-67 (78)
34 TIGR00116 tsf translation elon 45.3 94 0.002 25.8 6.6 61 58-118 6-66 (290)
35 PF10668 Phage_terminase: Phag 44.9 30 0.00064 22.3 2.9 28 59-86 24-51 (60)
36 PHA00327 minor capsid protein 44.6 16 0.00035 28.4 1.9 68 49-124 3-86 (187)
37 cd07922 CarBa CarBa is the A s 44.5 18 0.0004 24.6 1.9 32 77-110 9-40 (81)
38 PRK12332 tsf elongation factor 44.1 1.2E+02 0.0026 23.8 6.7 60 58-117 6-65 (198)
39 PF07793 DUF1631: Protein of u 43.1 39 0.00085 30.7 4.4 59 47-110 160-218 (729)
40 PF12826 HHH_2: Helix-hairpin- 43.1 26 0.00056 22.1 2.4 24 66-90 8-31 (64)
41 PRK01964 4-oxalocrotonate taut 42.8 7.7 0.00017 24.2 -0.1 33 47-79 12-44 (64)
42 cd04762 HTH_MerR-trunc Helix-T 42.8 33 0.00071 19.0 2.6 21 60-80 3-23 (49)
43 PF08938 HBS1_N: HBS1 N-termin 42.3 6.8 0.00015 26.0 -0.4 50 44-94 17-69 (79)
44 PF08281 Sigma70_r4_2: Sigma-7 41.8 34 0.00075 20.1 2.7 24 57-80 26-49 (54)
45 PRK02220 4-oxalocrotonate taut 41.3 48 0.001 20.0 3.4 33 46-78 11-43 (61)
46 PF03374 ANT: Phage antirepres 41.0 35 0.00075 23.3 3.0 28 59-86 26-53 (111)
47 PF00440 TetR_N: Bacterial reg 39.9 70 0.0015 18.5 3.9 28 59-90 18-45 (47)
48 TIGR00264 alpha-NAC-related pr 39.5 54 0.0012 23.9 3.9 32 55-86 77-108 (116)
49 PF12793 SgrR_N: Sugar transpo 39.4 34 0.00073 24.4 2.8 23 59-81 21-43 (115)
50 PRK06369 nac nascent polypepti 38.2 58 0.0013 23.6 3.8 33 56-88 76-108 (115)
51 PF09107 SelB-wing_3: Elongati 37.8 37 0.00081 20.8 2.4 23 59-81 12-34 (50)
52 cd07321 Extradiol_Dioxygenase_ 37.5 30 0.00064 23.0 2.1 27 86-113 16-42 (77)
53 PF03765 CRAL_TRIO_N: CRAL/TRI 37.2 92 0.002 18.6 5.8 25 68-92 28-52 (55)
54 cd04761 HTH_MerR-SF Helix-Turn 37.1 43 0.00093 19.0 2.6 22 60-81 3-24 (49)
55 PF09339 HTH_IclR: IclR helix- 36.9 44 0.00096 19.8 2.7 21 60-80 21-41 (52)
56 PF06078 DUF937: Bacterial pro 36.9 74 0.0016 22.8 4.3 34 47-80 90-125 (137)
57 PRK12449 acyl carrier protein; 36.6 67 0.0015 20.5 3.7 58 48-110 2-59 (80)
58 PF06059 DUF930: Domain of Unk 36.5 17 0.00037 25.7 0.8 22 108-129 45-66 (101)
59 PRK00116 ruvA Holliday junctio 36.4 57 0.0012 25.0 3.8 49 60-110 72-120 (192)
60 smart00419 HTH_CRP helix_turn_ 35.9 46 0.00099 18.6 2.5 22 60-81 11-32 (48)
61 PRK11235 bifunctional antitoxi 34.9 50 0.0011 22.3 2.9 28 53-80 9-36 (80)
62 PF13551 HTH_29: Winged helix- 34.4 37 0.0008 22.5 2.3 32 59-90 14-46 (112)
63 PF13411 MerR_1: MerR HTH fami 34.3 55 0.0012 20.0 2.9 22 60-81 3-24 (69)
64 PF00356 LacI: Bacterial regul 33.9 1.1E+02 0.0023 18.3 4.5 35 60-94 2-36 (46)
65 PF14771 DUF4476: Domain of un 33.5 88 0.0019 20.9 4.0 31 58-88 28-59 (95)
66 PF10975 DUF2802: Protein of u 33.4 54 0.0012 21.5 2.8 29 54-82 41-69 (70)
67 TIGR00013 taut 4-oxalocrotonat 33.0 57 0.0012 19.7 2.8 32 47-78 12-43 (63)
68 PF13542 HTH_Tnp_ISL3: Helix-t 32.9 63 0.0014 18.8 2.9 31 51-81 19-51 (52)
69 PRK01905 DNA-binding protein F 32.4 58 0.0012 21.3 2.9 32 51-82 41-75 (77)
70 PF03861 ANTAR: ANTAR domain; 31.6 1.1E+02 0.0023 18.6 3.9 28 54-81 13-40 (56)
71 PF06413 Neugrin: Neugrin; In 31.3 48 0.001 26.5 2.8 42 43-85 7-56 (225)
72 PF06972 DUF1296: Protein of u 30.5 1.5E+02 0.0034 19.1 4.6 43 55-97 4-47 (60)
73 COG5484 Uncharacterized conser 30.5 63 0.0014 26.8 3.3 31 59-89 21-51 (279)
74 PF09269 DUF1967: Domain of un 30.2 28 0.00061 22.5 1.1 47 73-119 17-67 (69)
75 PF04545 Sigma70_r4: Sigma-70, 30.0 78 0.0017 18.4 2.9 22 58-79 21-42 (50)
76 PF07746 LigA: Aromatic-ring-o 29.9 31 0.00067 23.7 1.3 32 77-111 4-35 (88)
77 PRK12547 RNA polymerase sigma 29.9 59 0.0013 23.4 2.8 23 58-80 129-151 (164)
78 PF08621 RPAP1_N: RPAP1-like, 29.8 1.2E+02 0.0026 18.6 3.8 30 45-80 13-42 (49)
79 PF08921 DUF1904: Domain of un 29.7 49 0.0011 23.5 2.3 34 42-75 4-37 (108)
80 TIGR03879 near_KaiC_dom probab 29.5 63 0.0014 21.5 2.6 24 57-80 32-55 (73)
81 PRK09047 RNA polymerase factor 28.9 64 0.0014 22.7 2.8 22 59-80 124-145 (161)
82 PHA03101 DNA topoisomerase typ 28.8 77 0.0017 26.8 3.6 28 49-76 246-273 (314)
83 PRK12529 RNA polymerase sigma 28.7 63 0.0014 23.7 2.8 21 59-79 145-165 (178)
84 PF01325 Fe_dep_repress: Iron 28.7 74 0.0016 19.9 2.8 21 60-80 25-45 (60)
85 TIGR02985 Sig70_bacteroi1 RNA 28.5 66 0.0014 22.3 2.8 22 59-80 131-152 (161)
86 PRK10244 anti-RssB factor; Pro 27.7 77 0.0017 22.0 2.9 32 51-82 47-79 (88)
87 PRK00745 4-oxalocrotonate taut 27.2 1.1E+02 0.0025 18.3 3.4 33 47-79 12-44 (62)
88 PF00376 MerR: MerR family reg 26.8 63 0.0014 18.5 2.0 16 60-75 2-17 (38)
89 smart00345 HTH_GNTR helix_turn 26.8 89 0.0019 18.0 2.8 20 60-79 23-42 (60)
90 CHL00098 tsf elongation factor 26.6 2.8E+02 0.0061 21.7 6.3 59 58-116 3-61 (200)
91 TIGR03793 TOMM_pelo TOMM prope 26.6 1.1E+02 0.0025 20.4 3.5 33 82-115 13-45 (77)
92 TIGR02384 RelB_DinJ addiction 26.6 83 0.0018 21.1 2.9 28 53-80 10-37 (83)
93 cd06170 LuxR_C_like C-terminal 26.5 92 0.002 17.6 2.8 22 58-79 16-37 (57)
94 smart00420 HTH_DEOR helix_turn 26.5 80 0.0017 17.7 2.5 22 59-80 16-37 (53)
95 TIGR02999 Sig-70_X6 RNA polyme 26.4 73 0.0016 23.1 2.8 23 58-80 151-173 (183)
96 PRK02289 4-oxalocrotonate taut 26.4 82 0.0018 19.3 2.7 32 46-77 11-42 (60)
97 TIGR03613 RutR pyrimidine util 26.4 1.1E+02 0.0024 22.4 3.8 32 59-94 30-61 (202)
98 PF04967 HTH_10: HTH DNA bindi 26.0 93 0.002 19.3 2.8 22 59-80 25-46 (53)
99 PRK00430 fis global DNA-bindin 25.9 85 0.0019 21.6 2.9 24 59-82 70-93 (95)
100 PRK09645 RNA polymerase sigma 25.7 74 0.0016 22.9 2.7 22 59-80 136-157 (173)
101 cd00092 HTH_CRP helix_turn_hel 25.4 82 0.0018 18.8 2.5 22 59-80 27-48 (67)
102 PF06385 Baculo_LEF-11: Baculo 25.3 84 0.0018 22.1 2.8 27 46-72 1-27 (94)
103 PRK09642 RNA polymerase sigma 25.1 81 0.0018 22.3 2.8 23 58-80 123-145 (160)
104 cd07377 WHTH_GntR Winged helix 25.0 98 0.0021 18.2 2.8 20 60-79 28-47 (66)
105 PF08220 HTH_DeoR: DeoR-like h 24.9 96 0.0021 19.0 2.8 21 59-79 16-36 (57)
106 PF01978 TrmB: Sugar-specific 24.8 99 0.0022 19.1 2.9 23 58-80 23-45 (68)
107 KOG3890|consensus 24.7 57 0.0012 28.0 2.1 32 41-72 72-103 (391)
108 PRK12530 RNA polymerase sigma 24.6 81 0.0018 23.4 2.8 23 58-80 151-173 (189)
109 cd04764 HTH_MlrA-like_sg1 Heli 24.5 1.1E+02 0.0023 18.9 3.0 18 60-77 3-20 (67)
110 PRK14996 TetR family transcrip 24.4 1.1E+02 0.0024 22.4 3.5 33 58-94 29-61 (192)
111 cd00491 4Oxalocrotonate_Tautom 24.3 1E+02 0.0022 18.1 2.8 32 47-78 11-42 (58)
112 TIGR02947 SigH_actino RNA poly 24.3 81 0.0018 23.3 2.8 23 58-80 148-170 (193)
113 PRK08402 replication factor A; 24.2 1.1E+02 0.0025 26.0 3.9 28 47-78 19-46 (355)
114 PRK13778 paaA phenylacetate-Co 24.0 2.9E+02 0.0062 23.3 6.2 63 52-115 192-260 (314)
115 PF04221 RelB: RelB antitoxin; 23.6 91 0.002 20.6 2.6 27 54-80 10-36 (83)
116 PF02796 HTH_7: Helix-turn-hel 23.6 82 0.0018 18.3 2.2 31 49-79 11-43 (45)
117 smart00741 SapB Saposin (B) Do 23.5 1.7E+02 0.0038 17.4 4.9 51 53-106 23-75 (76)
118 TIGR02156 PA_CoA_Oxy1 phenylac 23.5 3.1E+02 0.0067 22.8 6.2 59 52-111 174-237 (289)
119 PF01465 GRIP: GRIP domain; I 23.2 1.4E+02 0.003 17.8 3.1 24 55-78 23-46 (46)
120 smart00421 HTH_LUXR helix_turn 22.9 1.2E+02 0.0026 17.0 2.8 21 59-79 20-40 (58)
121 PF05331 DUF742: Protein of un 22.8 63 0.0014 23.2 1.8 22 58-79 56-77 (114)
122 cd01104 HTH_MlrA-CarA Helix-Tu 22.8 1.9E+02 0.0041 17.5 4.3 34 42-78 34-67 (68)
123 cd07923 Gallate_dioxygenase_C 22.7 89 0.0019 21.9 2.5 29 84-113 16-44 (94)
124 PF00633 HHH: Helix-hairpin-he 22.7 92 0.002 17.0 2.1 26 55-80 5-30 (30)
125 PF02561 FliS: Flagellar prote 22.5 1.6E+02 0.0035 20.6 3.9 49 53-101 52-102 (122)
126 PF13545 HTH_Crp_2: Crp-like h 22.4 70 0.0015 19.9 1.8 21 61-81 32-52 (76)
127 PF01028 Topoisom_I: Eukaryoti 22.4 1.3E+02 0.0027 24.2 3.6 30 47-76 177-206 (234)
128 TIGR02950 SigM_subfam RNA poly 22.3 1E+02 0.0022 21.5 2.8 23 58-80 122-144 (154)
129 TIGR02902 spore_lonB ATP-depen 22.1 1.4E+02 0.003 26.5 4.2 47 40-89 256-302 (531)
130 COG2042 Uncharacterized conser 22.0 1.5E+02 0.0032 23.2 3.8 29 65-94 126-160 (179)
131 PRK12516 RNA polymerase sigma 21.9 97 0.0021 23.1 2.8 24 59-82 134-157 (187)
132 PRK13756 tetracycline represso 21.8 1.2E+02 0.0026 23.3 3.3 32 59-94 26-57 (205)
133 TIGR02954 Sig70_famx3 RNA poly 21.8 99 0.0021 22.2 2.7 22 59-80 137-158 (169)
134 PRK12534 RNA polymerase sigma 21.7 92 0.002 22.7 2.6 23 58-80 154-176 (187)
135 PF03147 FDX-ACB: Ferredoxin-f 21.5 98 0.0021 20.7 2.5 26 45-70 67-92 (94)
136 TIGR01323 nitrile_alph nitrile 21.5 1.1E+02 0.0023 24.1 3.0 30 83-113 107-137 (185)
137 PRK12523 RNA polymerase sigma 21.3 1.1E+02 0.0023 22.2 2.8 22 59-80 137-158 (172)
138 PRK09644 RNA polymerase sigma 21.3 1E+02 0.0022 22.0 2.7 23 58-80 125-147 (165)
139 PRK03636 hypothetical protein; 21.2 1.8E+02 0.0038 22.6 4.1 53 73-129 11-71 (179)
140 smart00422 HTH_MERR helix_turn 21.2 1.1E+02 0.0024 18.6 2.6 24 60-83 3-26 (70)
141 PRK13626 transcriptional regul 21.1 84 0.0018 27.6 2.6 23 59-81 25-47 (552)
142 TIGR02394 rpoS_proteo RNA poly 21.1 50 0.0011 26.5 1.1 22 59-80 244-265 (285)
143 COG3415 Transposase and inacti 21.0 1E+02 0.0022 22.9 2.7 24 59-82 23-46 (138)
144 PRK12545 RNA polymerase sigma 20.9 1E+02 0.0022 23.1 2.8 21 59-79 157-177 (201)
145 smart00418 HTH_ARSR helix_turn 20.9 1.3E+02 0.0029 17.0 2.8 21 60-80 13-33 (66)
146 PRK12536 RNA polymerase sigma 20.8 1.1E+02 0.0023 22.4 2.8 23 58-80 146-168 (181)
147 TIGR02959 SigZ RNA polymerase 20.8 84 0.0018 22.8 2.2 22 59-80 118-139 (170)
148 PRK06759 RNA polymerase factor 20.7 1.1E+02 0.0025 21.3 2.8 23 58-80 123-145 (154)
149 PRK10668 DNA-binding transcrip 20.6 1.8E+02 0.0039 21.5 4.1 32 59-94 33-64 (215)
150 TIGR02952 Sig70_famx2 RNA poly 20.5 1.1E+02 0.0025 21.6 2.8 21 59-79 140-160 (170)
151 PRK09649 RNA polymerase sigma 20.5 1.1E+02 0.0024 22.6 2.8 22 59-80 148-169 (185)
152 PRK12542 RNA polymerase sigma 20.4 1.1E+02 0.0024 22.3 2.8 22 59-80 140-161 (185)
153 KOG3763|consensus 20.4 2.6E+02 0.0055 25.8 5.5 38 57-94 536-573 (585)
154 TIGR02948 SigW_bacill RNA poly 20.3 1.1E+02 0.0024 22.0 2.8 23 58-80 153-175 (187)
155 PF12674 Zn_ribbon_2: Putative 20.3 2.2E+02 0.0048 19.1 4.0 33 46-81 41-73 (81)
No 1
>KOG1815|consensus
Probab=98.95 E-value=1.3e-09 Score=93.57 Aligned_cols=77 Identities=30% Similarity=0.456 Sum_probs=71.2
Q ss_pred EecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCC---CcceeeeeecccC
Q psy7603 46 VLSTEEIVQHMIDCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTS---SGLVFSAVDFGSG 122 (130)
Q Consensus 46 vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~---~~~v~~~~~~~~~ 122 (130)
+|+.++|...|.+.|..|+++|++++.+|++||.||+|++++|+++|++ +++.++...|+... .+.+.+..|+++-
T Consensus 2 vl~~~~~~~~~~~~i~~~~~~ls~~~~~~~~ll~~~~W~~~kl~~~~~~-~~~~~~~~~g~~~~~~~~~~~~c~ic~~~~ 80 (444)
T KOG1815|consen 2 VLTPDDIAALMREDIIEVSDILSLSHAVARILLAHFCWNVEKLLEEWVE-DEETGCFFVGLLLWPKKKGDVQCGICVESY 80 (444)
T ss_pred CCchHhhhHHhHhhHHHHHHhhcCCHHHHHHHHHhcCcchHHHHHHHHh-cCcchhhhccccccCCCCccccCCcccCCC
Confidence 6889999999999999999999999999999999999999999999999 99999999997654 6778888888876
Q ss_pred C
Q psy7603 123 G 123 (130)
Q Consensus 123 ~ 123 (130)
.
T Consensus 81 ~ 81 (444)
T KOG1815|consen 81 D 81 (444)
T ss_pred c
Confidence 4
No 2
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=98.04 E-value=1.2e-05 Score=48.32 Aligned_cols=40 Identities=20% Similarity=0.344 Sum_probs=35.1
Q ss_pred HHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCCh
Q psy7603 57 IDCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQ 97 (130)
Q Consensus 57 ~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~ 97 (130)
++.|.+.++|+++++..|+-+|..++||.++-+..||+ ++
T Consensus 1 ~e~i~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~-~~ 40 (43)
T PF14555_consen 1 DEKIAQFMSITGADEDVAIQYLEANNWDLEAAVNAYFD-DG 40 (43)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHH-SS
T ss_pred CHHHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHh-CC
Confidence 36789999999999999999999999999999999999 54
No 3
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=92.73 E-value=0.4 Score=27.34 Aligned_cols=33 Identities=9% Similarity=0.167 Sum_probs=28.1
Q ss_pred HHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHH
Q psy7603 57 IDCIKEVNNVVEIPATTTRILLNHFKWDKEKLME 90 (130)
Q Consensus 57 ~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE 90 (130)
.+.|+++.+. |.++..|+.=|++.+||.++.++
T Consensus 3 ~~~v~~L~~m-Gf~~~~~~~AL~~~~~nve~A~~ 35 (37)
T PF00627_consen 3 EEKVQQLMEM-GFSREQAREALRACNGNVERAVD 35 (37)
T ss_dssp HHHHHHHHHH-TS-HHHHHHHHHHTTTSHHHHHH
T ss_pred HHHHHHHHHc-CCCHHHHHHHHHHcCCCHHHHHH
Confidence 3568888888 99999999999999999998765
No 4
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=92.56 E-value=0.66 Score=30.15 Aligned_cols=42 Identities=12% Similarity=0.336 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 53 VQHMIDCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 53 ~~~~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
...+.+.|..++..+++...-++.+|..-+||.++.+..|-+
T Consensus 9 ~~~q~~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 9 SPEQQEMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred CHHHHHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 346778899999999999999999999999999999998887
No 5
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=92.08 E-value=0.11 Score=32.26 Aligned_cols=38 Identities=11% Similarity=0.323 Sum_probs=33.5
Q ss_pred HHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 57 IDCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 57 ~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
++.|..++...++.+.-|+..|...+||-++.+..|..
T Consensus 1 q~mv~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~ 38 (51)
T PF03943_consen 1 QEMVQQFSQQTGMNLEWSQKCLEENNWDYERALQNFEE 38 (51)
T ss_dssp HHHHHHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 35789999999999999999999999999999999988
No 6
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=91.55 E-value=0.78 Score=25.86 Aligned_cols=35 Identities=11% Similarity=0.158 Sum_probs=28.8
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYY 93 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~ 93 (130)
+.|+++.+ +|.+...|+.-|+..+||.++.++-.+
T Consensus 3 ~~v~~L~~-mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLE-MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHH-cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 34566666 599999999999999999999887655
No 7
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=89.43 E-value=1.4 Score=24.71 Aligned_cols=33 Identities=12% Similarity=0.046 Sum_probs=26.5
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDKEKLMERY 92 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y 92 (130)
.|+++.+. |.++..|+.-|+..+||.++.++-.
T Consensus 4 ~v~~L~~m-Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 4 KIDQLLEM-GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHc-CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 45555554 9999999999999999999887643
No 8
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=86.63 E-value=2.7 Score=24.46 Aligned_cols=37 Identities=8% Similarity=0.254 Sum_probs=30.7
Q ss_pred HHHHHHhhhh-CCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 58 DCIKEVNNVV-EIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 58 e~I~~V~~iL-~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
+.|..+.+++ ++++...+..|+.+++|++..++...+
T Consensus 3 ~~v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 3 EMVQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 4577788887 689999999999999999999887664
No 9
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=81.04 E-value=7.3 Score=22.63 Aligned_cols=38 Identities=5% Similarity=0.218 Sum_probs=31.3
Q ss_pred HHHHHHHhhhh-CCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 57 IDCIKEVNNVV-EIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 57 ~e~I~~V~~iL-~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
.+.|..+.+++ ++++..++..|+.++.|++..++...+
T Consensus 3 ~~~v~~L~~mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 3 DEALHDLKDMFPNLDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 34566677776 689999999999999999999887765
No 10
>KOG3154|consensus
Probab=77.55 E-value=3.3 Score=33.70 Aligned_cols=31 Identities=26% Similarity=0.569 Sum_probs=24.0
Q ss_pred CHHHHHHHHHhCCCCh------HHHHHHHhc-CChhhH
Q psy7603 70 PATTTRILLNHFKWDK------EKLMERYYD-GDQESS 100 (130)
Q Consensus 70 s~~~A~lLL~~fkWn~------ekLlE~y~e-~D~~kv 100 (130)
-+..|++||.+|+|-. ..|++.|-. .++..|
T Consensus 162 ~~e~A~~lL~~F~wG~~Fl~lN~~lLd~Ya~C~~s~ev 199 (263)
T KOG3154|consen 162 FPEEARELLDKFKWGHAFLELNKDLLDEYAKCASSAEV 199 (263)
T ss_pred ChhHHHHHHhcCcchHHHHHHhHHHHHHHHhhCCHHHH
Confidence 3679999999999987 568888876 565544
No 11
>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=75.26 E-value=3.9 Score=25.93 Aligned_cols=31 Identities=26% Similarity=0.516 Sum_probs=27.1
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCChHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDKEKLM 89 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLl 89 (130)
.+.+|+..|+|++....--...|+|+.-.-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~~ 45 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKDRYKWDELLPI 45 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHHhhCccccCch
Confidence 4788999999999999999999999985444
No 12
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=67.78 E-value=15 Score=27.65 Aligned_cols=66 Identities=11% Similarity=0.138 Sum_probs=42.7
Q ss_pred HHHHHHhhhhCCCHHHH-HHHHHhCCCChHHHHH--HHhcCChhhHH---HHcCCCCCCcceeeeeecccCC
Q psy7603 58 DCIKEVNNVVEIPATTT-RILLNHFKWDKEKLME--RYYDGDQESST---LDYSASTSSGLVFSAVDFGSGG 123 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A-~lLL~~fkWn~ekLlE--~y~e~D~~kvl---~~aGl~~~~~~v~~~~~~~~~~ 123 (130)
+..+.++.||+|+.+.| |.|-=.-.|+...|.. ++|.-.++.++ ...|+.|-...-..++-|.-|+
T Consensus 23 ~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~d~l~g~~~~~~~~p~~~~~~~~ai~~~g~ 94 (147)
T PF08667_consen 23 KHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSPDELFGHSDNSGQNPAAQNEMQDAIFYIGS 94 (147)
T ss_pred hhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCHHHHHhhhhcccCCcchhhHHHhhhhhccc
Confidence 56789999999999999 5565678899865433 33443778888 5677766232223333344443
No 13
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=65.05 E-value=7.4 Score=22.78 Aligned_cols=26 Identities=12% Similarity=0.224 Sum_probs=18.3
Q ss_pred HHHHHHHhhhhCCCHHHHHHHHHhCC
Q psy7603 57 IDCIKEVNNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 57 ~e~I~~V~~iL~vs~~~A~lLL~~fk 82 (130)
...+.+|+..|+|++......++.|+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 45788999999999999998888774
No 14
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=64.61 E-value=10 Score=23.73 Aligned_cols=37 Identities=22% Similarity=0.185 Sum_probs=33.0
Q ss_pred EecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhCC
Q psy7603 46 VLSTEEIVQHMIDCIKEVNNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 46 vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~fk 82 (130)
-|+.++|.+.+.--+.+++..|+|+.+.-..+-|.++
T Consensus 4 ~lt~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~G 40 (52)
T PF02042_consen 4 SLTLEDLSQYFHLPIKEAAKELGVSVTTLKRRCRRLG 40 (52)
T ss_pred ccCHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 4789999999999999999999999998888877765
No 15
>PF04034 DUF367: Domain of unknown function (DUF367); InterPro: IPR007177 This domain is found in a family of proteins of unknown function. It appears to be found in eukaryotes and archaebacteria, and occurs associated with a potential metal-binding region in RNase L inhibitor, RLI (IPR007209 from INTERPRO).
Probab=63.71 E-value=13 Score=27.39 Aligned_cols=53 Identities=19% Similarity=0.317 Sum_probs=33.8
Q ss_pred cccceEEecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhCCCCh------HHHHHHHhc-CChhhHH
Q psy7603 40 EEFVFEVLSTEEIVQHMIDCIKEVNNVVEIPATTTRILLNHFKWDK------EKLMERYYD-GDQESST 101 (130)
Q Consensus 40 ~~~~y~vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~------ekLlE~y~e-~D~~kvl 101 (130)
+..+|+-=+.+-| .-.-=|+|.. ..|..||.+|+|-. ..|+++|-. .+.+.+.
T Consensus 60 YGkP~kLscvEAl--------AAaLyI~G~~-~~A~~lL~~FkWG~~F~~LN~elLe~Y~~~~~~~ev~ 119 (127)
T PF04034_consen 60 YGKPCKLSCVEAL--------AAALYILGFK-EQAEELLSKFKWGHTFLELNKELLEAYAKCKTSEEVI 119 (127)
T ss_pred cCCcccccHHHHH--------HHHHHHcCCH-HHHHHHHhcCCCcHHHHHHHHHHHHHHHcCCCHHHHH
Confidence 5556663344333 2233466665 58888999999987 467888876 5555554
No 16
>PF10245 MRP-S22: Mitochondrial 28S ribosomal protein S22; InterPro: IPR019374 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 is the conserved N terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them [].
Probab=62.50 E-value=10 Score=30.98 Aligned_cols=33 Identities=9% Similarity=0.436 Sum_probs=31.3
Q ss_pred CcccceEEecHHHHHHHHHHHHHHHhhhhCCCH
Q psy7603 39 VEEFVFEVLSTEEIVQHMIDCIKEVNNVVEIPA 71 (130)
Q Consensus 39 ~~~~~y~vLs~~eI~~~~~e~I~~V~~iL~vs~ 71 (130)
.....|+-||.+|+.+.+.+.+.+....|++||
T Consensus 32 ~~~p~yklMTdeql~~~~~~~~~~a~~~LqMPP 64 (243)
T PF10245_consen 32 LKPPTYKLMTDEQLEEALEKAIEKAKKLLQMPP 64 (243)
T ss_pred CCCCeeEeCCHHHHHHHHHHHHHHHHHhcCCCC
Confidence 477889999999999999999999999999999
No 17
>PRK04217 hypothetical protein; Provisional
Probab=62.39 E-value=28 Score=24.91 Aligned_cols=52 Identities=12% Similarity=0.035 Sum_probs=37.2
Q ss_pred cccceEEecHHHHHHHHHHH-----HHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 40 EEFVFEVLSTEEIVQHMIDC-----IKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 40 ~~~~y~vLs~~eI~~~~~e~-----I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
...+-..|+.++......-. +.+|+.+|+|+.......|+. -..+|.+.+..
T Consensus 36 ~~~p~~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~R---ArkkLre~L~~ 92 (110)
T PRK04217 36 PPKPPIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTS---ARKKVAQMLVE 92 (110)
T ss_pred CCCCcccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH---HHHHHHHHHHh
Confidence 34456678888765544443 789999999999999999887 45555555544
No 18
>PF05138 PaaA_PaaC: Phenylacetic acid catabolic protein; InterPro: IPR007814 This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid []. These proteins may form part of a dioxygenase complex.; PDB: 3PWQ_K 3PVT_B 1OTK_B 3PW1_B 3PW8_B 3PVR_B 3PVY_B 3Q1G_A 3PF7_B 3PM5_C ....
Probab=59.98 E-value=13 Score=30.11 Aligned_cols=61 Identities=8% Similarity=0.009 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCC
Q psy7603 49 TEEIVQHMIDCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTSS 110 (130)
Q Consensus 49 ~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~ 110 (130)
.+.+++.++.....+..+++.+.....+.-.--.++.+.|-++|.. .-..+|.++||..|.
T Consensus 167 ~~r~q~Al~~~wp~~~elF~~~~~~~~l~~~~~~~~~~~lr~~w~~-~v~~~l~~~gL~~P~ 227 (263)
T PF05138_consen 167 RERMQAALDRLWPYTLELFGPDDSEEALAWGGRAPDNEELRQRWLA-EVVPVLEEAGLEVPE 227 (263)
T ss_dssp HHHHHHHHHHHHHHHHHCC-S-HCHHHHHCTTSSS-HHHHHHHHHH-HHHHHHHHTT---S-
T ss_pred HHHHHHHHHHHHHHHHHHcCCCchHHHHHHCCCCCCHHHHHHHHHH-HHHHHHHHcCCCCCC
Confidence 4556667777777888999999888443334457999999999999 999999999998887
No 19
>PF12728 HTH_17: Helix-turn-helix domain
Probab=57.57 E-value=13 Score=21.92 Aligned_cols=21 Identities=19% Similarity=0.328 Sum_probs=17.8
Q ss_pred HHHHhhhhCCCHHHHHHHHHh
Q psy7603 60 IKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~ 80 (130)
+.+++++|+|++...+-+++.
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 678999999999998888753
No 20
>PF15586 Imm47: Immunity protein 47
Probab=56.66 E-value=22 Score=25.52 Aligned_cols=40 Identities=10% Similarity=0.136 Sum_probs=21.8
Q ss_pred CCCcccccc--cccCCCCCCCCCCCcccceEEecHHHHHHHHHH
Q psy7603 17 SSDDIGYAM--EVENQNPKDRQNDVEEFVFEVLSTEEIVQHMID 58 (130)
Q Consensus 17 ~~~d~d~~~--e~~~~~~~~~~~~~~~~~y~vLs~~eI~~~~~e 58 (130)
+++-++|+. .......+.. -.+.+...|.||+=|.+....
T Consensus 20 Ped~~~F~~~l~l~IG~~~~~--G~d~F~v~VcTP~wL~~~~~~ 61 (116)
T PF15586_consen 20 PEDPDNFCFWLELDIGPEGED--GSDYFQVFVCTPKWLSKNCWK 61 (116)
T ss_pred CCCCcceEEEEEEEECCCCCC--ccceEEEEEEcHHHHHHhhcC
Confidence 444466663 3333333322 256677788888777665444
No 21
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=55.09 E-value=17 Score=23.38 Aligned_cols=31 Identities=16% Similarity=0.354 Sum_probs=22.5
Q ss_pred HHHHHHHHH-----HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 50 EEIVQHMID-----CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 50 ~eI~~~~~e-----~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
++|...+++ ...+|++.++|+...||.+|.+
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 345555555 4678999999999999988864
No 22
>PRK11426 hypothetical protein; Provisional
Probab=53.07 E-value=23 Score=26.33 Aligned_cols=38 Identities=13% Similarity=0.233 Sum_probs=33.1
Q ss_pred eEEecHHHHHHHHH-HHHHHHhhhhCCCHHHHHHHHHhC
Q psy7603 44 FEVLSTEEIVQHMI-DCIKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 44 y~vLs~~eI~~~~~-e~I~~V~~iL~vs~~~A~lLL~~f 81 (130)
..-+++++|...+- +.|++++.-+++++..+.-.|..+
T Consensus 58 N~pIs~~ql~~~lG~d~i~~lA~q~Gl~~~~~~~~LA~~ 96 (132)
T PRK11426 58 NQSVSGEQLESALGTNAVSDLGQKLGVDTSTASSLLAEQ 96 (132)
T ss_pred CCCCCHHHHHHHhChHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 45689999999986 789999999999999998887654
No 23
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=50.40 E-value=24 Score=20.37 Aligned_cols=23 Identities=13% Similarity=0.212 Sum_probs=18.3
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhC
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~f 81 (130)
.+.+++..|||++..-..-|++|
T Consensus 20 n~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 20 NVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHC
T ss_pred CHHHHHHHHCCCHHHHHHHHHhC
Confidence 47889999999999988888776
No 24
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=50.27 E-value=22 Score=19.95 Aligned_cols=21 Identities=14% Similarity=0.292 Sum_probs=17.4
Q ss_pred HHHHhhhhCCCHHHHHHHHHh
Q psy7603 60 IKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~ 80 (130)
+.+++..|+|++.....|++.
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHc
Confidence 678999999999988877653
No 25
>PF13518 HTH_28: Helix-turn-helix domain
Probab=49.32 E-value=16 Score=21.20 Aligned_cols=24 Identities=13% Similarity=0.347 Sum_probs=20.2
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCC
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fk 82 (130)
-+.+|+..++|++......++.|+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 578899999999999888877764
No 26
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=48.53 E-value=45 Score=21.62 Aligned_cols=47 Identities=9% Similarity=0.156 Sum_probs=30.6
Q ss_pred HHHHHHHhCCCChHHHHHHHhc----CChhhHHHHcCCCCCCcceeeeeec
Q psy7603 73 TTRILLNHFKWDKEKLMERYYD----GDQESSTLDYSASTSSGLVFSAVDF 119 (130)
Q Consensus 73 ~A~lLL~~fkWn~ekLlE~y~e----~D~~kvl~~aGl~~~~~~v~~~~~~ 119 (130)
.-..|+..++|+.+.-+.+|.. ..-++.|+++|+.+.....+...-|
T Consensus 17 ~ier~~~~~~~~~~e~~~~f~~~L~~~Gv~~~L~~~G~~~GD~V~Ig~~eF 67 (69)
T TIGR03595 17 KIERWVAKTPFNNDENLRRFARKLKKLGVEDALRKAGAKDGDTVRIGDFEF 67 (69)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHCCHHHHHHHcCCCCCCEEEEccEEE
Confidence 3444566666666544444433 4568889999999988777765554
No 27
>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=48.08 E-value=15 Score=20.71 Aligned_cols=21 Identities=10% Similarity=0.341 Sum_probs=16.7
Q ss_pred HHHhhhhCCCHHHHHHHHHhC
Q psy7603 61 KEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 61 ~~V~~iL~vs~~~A~lLL~~f 81 (130)
++|++.|++++.....+|.++
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHhCCcHHHHHHHHHHH
Confidence 568899999999998888765
No 28
>PRK09624 porD pyuvate ferredoxin oxidoreductase subunit delta; Reviewed
Probab=47.69 E-value=12 Score=26.13 Aligned_cols=15 Identities=33% Similarity=0.565 Sum_probs=14.0
Q ss_pred hCCCChHHHHHHHhc
Q psy7603 80 HFKWDKEKLMERYYD 94 (130)
Q Consensus 80 ~fkWn~ekLlE~y~e 94 (130)
-|+||-+++.+.|+.
T Consensus 5 ~~~~~~~~~~~~~~~ 19 (105)
T PRK09624 5 PFKADIERVQKEYSE 19 (105)
T ss_pred cccccHHHHHHHHHH
Confidence 389999999999999
No 29
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=47.50 E-value=40 Score=21.15 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=24.3
Q ss_pred HHHHHHHHhhhhCCCHHHHHHHHHhCC
Q psy7603 56 MIDCIKEVNNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 56 ~~e~I~~V~~iL~vs~~~A~lLL~~fk 82 (130)
..-.|+..+.-+++|+..|.-+|.+++
T Consensus 4 ~v~~Ie~~A~~~~~s~~ea~~~~~~~~ 30 (62)
T PF12668_consen 4 VVFCIEEFAKKLNISGEEAYNYFKRSG 30 (62)
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHcC
Confidence 455899999999999999999999887
No 30
>PRK02287 hypothetical protein; Provisional
Probab=46.68 E-value=34 Score=26.42 Aligned_cols=38 Identities=21% Similarity=0.434 Sum_probs=26.7
Q ss_pred HhhhhCCCHHHHHHHHHhCCCCh------HHHHHHHhc-CChhhHH
Q psy7603 63 VNNVVEIPATTTRILLNHFKWDK------EKLMERYYD-GDQESST 101 (130)
Q Consensus 63 V~~iL~vs~~~A~lLL~~fkWn~------ekLlE~y~e-~D~~kvl 101 (130)
.--|+|.. +.|..||.+|+|-. ..++++|-. .+.+.+.
T Consensus 116 aLyI~G~~-~~A~~ll~~F~WG~~Fl~lN~elLe~Y~~~~~~~ev~ 160 (171)
T PRK02287 116 ALYILGFK-EEAEKILSKFKWGHTFLELNKEPLEAYARAKDSEEIV 160 (171)
T ss_pred HHHHcCCH-HHHHHHHhhCCChHHHHHHHHHHHHHHHccCCHHHHH
Confidence 33456654 48888999999987 467888875 5555554
No 31
>PRK09377 tsf elongation factor Ts; Provisional
Probab=45.43 E-value=85 Score=26.06 Aligned_cols=60 Identities=18% Similarity=0.146 Sum_probs=50.1
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCCcceeeee
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTSSGLVFSAV 117 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~~~v~~~~ 117 (130)
+.|.++...+|.+--.|+-=|...+||.++.++-.....-.+.-+++|=...+++|.+.+
T Consensus 7 ~~IK~LR~~Tgagm~dCKkAL~e~~gD~ekAi~~Lrk~G~akA~Kk~~R~a~EG~I~~~~ 66 (290)
T PRK09377 7 ALVKELRERTGAGMMDCKKALTEADGDIEKAIEWLRKKGLAKAAKKAGRVAAEGLVAAKV 66 (290)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhchhhHHHhcCccccceEEEEEe
Confidence 568899999999999999999999999999998777645566777777777888887644
No 32
>TIGR02158 PA_CoA_Oxy3 phenylacetate-CoA oxygenase, PaaI subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=45.38 E-value=1.1e+02 Score=24.73 Aligned_cols=62 Identities=5% Similarity=0.022 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCCcc
Q psy7603 50 EEIVQHMIDCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTSSGL 112 (130)
Q Consensus 50 ~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~~~ 112 (130)
+.++..++..--.+.++++.++....+.=.-.+=+.+.|-.+|.. .-..+|.++||..|...
T Consensus 142 ~r~Q~Ald~~wp~~~elF~~~~~~~~l~~~Gi~~~~~~Lr~~w~~-~v~~~l~~agL~~P~~~ 203 (237)
T TIGR02158 142 RRLQEALNELWPYTAELFEAGPIDEELAEAGIAVDPATLQAAWEK-EVNAVLNEATLTLPQQT 203 (237)
T ss_pred HHHHHHHHHHHHHHHHHcCCCchHHHHHHcCCCCCHHHHHHHHHH-HHHHHHHHhCCCCCCCc
Confidence 445556666666778889988865432222233356889999999 99999999999888754
No 33
>PHA00675 hypothetical protein
Probab=45.34 E-value=82 Score=21.44 Aligned_cols=55 Identities=7% Similarity=-0.106 Sum_probs=40.2
Q ss_pred CCCCCCCCCcccceEEecHHHHHHHHHHH------HHHHhhhhCCCHHHHHHHHHhCCCCh
Q psy7603 31 NPKDRQNDVEEFVFEVLSTEEIVQHMIDC------IKEVNNVVEIPATTTRILLNHFKWDK 85 (130)
Q Consensus 31 ~~~~~~~~~~~~~y~vLs~~eI~~~~~e~------I~~V~~iL~vs~~~A~lLL~~fkWn~ 85 (130)
.+..+....+..+---||..+++...... ...|+.-++||++....+.+...|-.
T Consensus 7 ~~~~~~~~Ge~h~~AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~W~~ 67 (78)
T PHA00675 7 VNDAGLRVGEDHPNAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYERRGQ 67 (78)
T ss_pred cccccccCCCCCCCcccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccchhhh
Confidence 34444444455666779998887665554 23788999999999999999999964
No 34
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=45.30 E-value=94 Score=25.82 Aligned_cols=61 Identities=13% Similarity=0.145 Sum_probs=51.2
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCCcceeeeee
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTSSGLVFSAVD 118 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~~~v~~~~~ 118 (130)
+.|.++.+.+|.+--.|+-=|...+||.++.++-.....-.+.-+++|=...+++|.+.++
T Consensus 6 ~~IK~LRe~Tgagm~dCKkAL~e~~gDiekAi~~LRkkG~akA~Kk~~R~a~EG~V~~~~~ 66 (290)
T TIGR00116 6 QLVKELRERTGAGMMDCKKALTEANGDFEKAIKNLRESGIAKAAKKADRVAAEGVIVLKSD 66 (290)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhchhHHHHhcccccCCcEEEEEEc
Confidence 4588999999999999999999999999999987777555667777887788888877663
No 35
>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=44.89 E-value=30 Score=22.31 Aligned_cols=28 Identities=21% Similarity=0.443 Sum_probs=25.1
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCChH
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDKE 86 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~e 86 (130)
...+|++.|+|++.+.+--=...+|+..
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~~dkW~~~ 51 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKSRDKWDEK 51 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhhhcchhhH
Confidence 5788999999999999999999999873
No 36
>PHA00327 minor capsid protein
Probab=44.62 E-value=16 Score=28.39 Aligned_cols=68 Identities=13% Similarity=0.185 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhCC-------------CCh---HHHHHHHhcCChhhHHHHcCCCCCCcc
Q psy7603 49 TEEIVQHMIDCIKEVNNVVEIPATTTRILLNHFK-------------WDK---EKLMERYYDGDQESSTLDYSASTSSGL 112 (130)
Q Consensus 49 ~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~fk-------------Wn~---ekLlE~y~e~D~~kvl~~aGl~~~~~~ 112 (130)
++.+-...-..|.-|.+=|++=|++|.-||-++. |++ |++-..=|. -.-+=+++|||.|-
T Consensus 3 pelv~~~agaav~gvas~lgml~g~asg~l~Y~gaqkqNa~~~~ia~rqmafQErMSnTA~q-R~~eDmkkAGLNpL--- 78 (187)
T PHA00327 3 PELVTNTAGAAVSGVASGLGMLPGIASGVLGYLGAQKQNATAKQIARRQMAFQERMSNTAYQ-RAMEDMKKAGLNPL--- 78 (187)
T ss_pred HHHHhhhhchhhhhhhhccccccchhhhhHHHHHHHhhhHHHHHHHHHHHHHHHHhhhHHHH-HHHHHHHHcCccHH---
Confidence 4555566667788888989999999999998874 433 333322222 23456889999663
Q ss_pred eeeeeecccCCc
Q psy7603 113 VFSAVDFGSGGS 124 (130)
Q Consensus 113 v~~~~~~~~~~~ 124 (130)
++||+||+
T Consensus 79 ----la~g~GgA 86 (187)
T PHA00327 79 ----LAFGKGGA 86 (187)
T ss_pred ----HHhcCCCC
Confidence 46776664
No 37
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=44.45 E-value=18 Score=24.58 Aligned_cols=32 Identities=25% Similarity=0.432 Sum_probs=24.0
Q ss_pred HHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCC
Q psy7603 77 LLNHFKWDKEKLMERYYDGDQESSTLDYSASTSS 110 (130)
Q Consensus 77 LL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~ 110 (130)
|+++..++- .+.++|-+ ||+.++.++||.+.+
T Consensus 9 li~~L~~dp-~~rerF~~-DPea~~~~~gLt~eE 40 (81)
T cd07922 9 LIQELFKDP-GLIERFQD-DPSAVFEEYGLTPAE 40 (81)
T ss_pred HHHHHhcCH-HHHHHHHH-CHHHHHHHcCCCHHH
Confidence 444444433 47899999 999999999997755
No 38
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=44.09 E-value=1.2e+02 Score=23.76 Aligned_cols=60 Identities=18% Similarity=0.150 Sum_probs=49.6
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCCcceeeee
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTSSGLVFSAV 117 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~~~v~~~~ 117 (130)
..|.++.+.++.+--.|+-=|...+||.++.++-.....-.+.-+++|=....+++.+.+
T Consensus 6 ~~ik~LR~~tga~~~~ck~AL~~~~gd~~~A~~~lr~~g~~~a~kk~~r~~~eG~i~~~i 65 (198)
T PRK12332 6 KLVKELREKTGAGMMDCKKALEEANGDMEKAIEWLREKGLAKAAKKAGRVAAEGLVGSYI 65 (198)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhhhhHHHHhccccccCceEEEEE
Confidence 468899999999999999999999999999998777645566777777777777776654
No 39
>PF07793 DUF1631: Protein of unknown function (DUF1631); InterPro: IPR012434 The members of this family are sequences derived from a group of hypothetical proteins expressed by certain bacterial species. The region concerned is approximately 440 amino acid residues in length.
Probab=43.13 E-value=39 Score=30.75 Aligned_cols=59 Identities=10% Similarity=0.184 Sum_probs=50.9
Q ss_pred ecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCC
Q psy7603 47 LSTEEIVQHMIDCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTSS 110 (130)
Q Consensus 47 Ls~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~ 110 (130)
|.|..|...+.+.+. -++++.....+||+.|.=..-.-+...|. .-+.+|+++||.|.-
T Consensus 160 l~P~~l~~al~~a~~----~l~~~~~~~l~l~~~f~~~l~~~L~~lY~-~lN~~L~~~GVlP~l 218 (729)
T PF07793_consen 160 LGPEALCRALREALE----QLGLDREVRLILYKLFERQLMAELGALYA-ELNRLLIEAGVLPDL 218 (729)
T ss_pred CCHHHHHHHHHHHHH----HCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHcCCCCCc
Confidence 678888887777664 56899999999999999999889999999 999999999997644
No 40
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=43.07 E-value=26 Score=22.14 Aligned_cols=24 Identities=29% Similarity=0.515 Sum_probs=17.9
Q ss_pred hhCCCHHHHHHHHHhCCCChHHHHH
Q psy7603 66 VVEIPATTTRILLNHFKWDKEKLME 90 (130)
Q Consensus 66 iL~vs~~~A~lLL~~fkWn~ekLlE 90 (130)
|=+|.+..|+.|++||+ +.+.|+.
T Consensus 8 I~~VG~~~ak~L~~~f~-sl~~l~~ 31 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFG-SLEALMN 31 (64)
T ss_dssp STT--HHHHHHHHHCCS-CHHHHCC
T ss_pred CCCccHHHHHHHHHHcC-CHHHHHH
Confidence 44677999999999999 7776654
No 41
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=42.79 E-value=7.7 Score=24.16 Aligned_cols=33 Identities=15% Similarity=0.423 Sum_probs=27.9
Q ss_pred ecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHH
Q psy7603 47 LSTEEIVQHMIDCIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 47 Ls~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~ 79 (130)
.|.++.++......+.++..|++|+....+++.
T Consensus 12 rt~eqk~~l~~~it~~l~~~lg~p~~~v~V~i~ 44 (64)
T PRK01964 12 RPEEKIKNLIREVTEAISATLDVPKERVRVIVN 44 (64)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcChhhEEEEEE
Confidence 578899999999999999999999987766554
No 42
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=42.79 E-value=33 Score=19.00 Aligned_cols=21 Identities=19% Similarity=0.332 Sum_probs=16.4
Q ss_pred HHHHhhhhCCCHHHHHHHHHh
Q psy7603 60 IKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~ 80 (130)
+.+|+..|+|++...+.+.+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 578899999999887766543
No 43
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=42.31 E-value=6.8 Score=26.02 Aligned_cols=50 Identities=24% Similarity=0.425 Sum_probs=36.8
Q ss_pred eEEecHHHHHHHHHHHHHHHhhhhCC---CHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 44 FEVLSTEEIVQHMIDCIKEVNNVVEI---PATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 44 y~vLs~~eI~~~~~e~I~~V~~iL~v---s~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
..-||+++-. +|.+.+.+|.++|+= |....+--|.||.+++++-+.-...
T Consensus 17 ~~~Ls~ed~~-~L~~~l~~vr~~Lg~~~~~e~~i~eal~~~~fDvekAl~~Ll~ 69 (79)
T PF08938_consen 17 EDELSPEDQA-QLYSCLPQVREVLGDYVPPEEQIKEALWHYYFDVEKALDYLLS 69 (79)
T ss_dssp HHH-TCHHHH-HHCHHCCCHHHHCCCCC--CCHHHHHHHHTTT-CCHHHHHHHH
T ss_pred cccCCHHHHH-HHHHHHHHHHHHHcccCCCHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 3447776654 488889999999985 6677788899999999998876655
No 44
>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=41.84 E-value=34 Score=20.15 Aligned_cols=24 Identities=17% Similarity=0.200 Sum_probs=17.2
Q ss_pred HHHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 57 IDCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 57 ~e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.....+|+.++++|+..++..|+.
T Consensus 26 g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 26 GMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp ---HHHHHHHCTS-HHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 345788999999999999887753
No 45
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=41.29 E-value=48 Score=20.03 Aligned_cols=33 Identities=15% Similarity=0.234 Sum_probs=27.5
Q ss_pred EecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHH
Q psy7603 46 VLSTEEIVQHMIDCIKEVNNVVEIPATTTRILL 78 (130)
Q Consensus 46 vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL 78 (130)
..|.++.++......+.++..+++|+....+++
T Consensus 11 Grs~eqk~~l~~~it~~l~~~~~~p~~~v~V~i 43 (61)
T PRK02220 11 GRTEEQLKALVKDVTAAVSKNTGAPAEHIHVII 43 (61)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCcChhhEEEEE
Confidence 458899999999999999999999987765544
No 46
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=41.03 E-value=35 Score=23.32 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=23.6
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCChH
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDKE 86 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~e 86 (130)
.|.+++.+|+|++..-.-+|+..+|=--
T Consensus 26 ti~~~AK~L~i~~~~l~~~Lr~~g~l~~ 53 (111)
T PF03374_consen 26 TIREAAKLLGIGRNKLFQWLREKGWLYR 53 (111)
T ss_pred cHHHHHHHhCCCHHHHHHHHHhCCceEE
Confidence 3678888889999999999999888443
No 47
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=39.87 E-value=70 Score=18.49 Aligned_cols=28 Identities=14% Similarity=0.406 Sum_probs=19.4
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCChHHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDKEKLME 90 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE 90 (130)
.+++|+.-++|++.. |-+||. |++.|+.
T Consensus 18 s~~~Ia~~~gvs~~~---~y~~f~-~k~~l~~ 45 (47)
T PF00440_consen 18 SIRDIARRAGVSKGS---FYRYFP-SKDDLLR 45 (47)
T ss_dssp SHHHHHHHHTSCHHH---HHHHCS-SHHHHHH
T ss_pred CHHHHHHHHccchhh---HHHHcC-CHHHHHh
Confidence 367788888998864 456666 6666654
No 48
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=39.50 E-value=54 Score=23.86 Aligned_cols=32 Identities=19% Similarity=0.069 Sum_probs=27.7
Q ss_pred HHHHHHHHHhhhhCCCHHHHHHHHHhCCCChH
Q psy7603 55 HMIDCIKEVNNVVEIPATTTRILLNHFKWDKE 86 (130)
Q Consensus 55 ~~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~e 86 (130)
.=.+.|.-|++-.+++...|+--|...+||.-
T Consensus 77 i~~eDI~lV~eq~gvs~e~A~~AL~~~~gDl~ 108 (116)
T TIGR00264 77 ITEDDIELVMKQCNVSKEEARRALEECGGDLA 108 (116)
T ss_pred CCHHHHHHHHHHhCcCHHHHHHHHHHcCCCHH
Confidence 34567788899999999999999999999973
No 49
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=39.41 E-value=34 Score=24.40 Aligned_cols=23 Identities=17% Similarity=0.338 Sum_probs=20.9
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhC
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~f 81 (130)
.|.+|+++|.+|+-.|++||++.
T Consensus 21 tl~elA~~l~cS~Rn~r~lLkkm 43 (115)
T PF12793_consen 21 TLDELAELLFCSRRNARTLLKKM 43 (115)
T ss_pred eHHHHHHHhCCCHHHHHHHHHHH
Confidence 58899999999999999999864
No 50
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=38.23 E-value=58 Score=23.63 Aligned_cols=33 Identities=15% Similarity=0.065 Sum_probs=28.0
Q ss_pred HHHHHHHHhhhhCCCHHHHHHHHHhCCCChHHH
Q psy7603 56 MIDCIKEVNNVVEIPATTTRILLNHFKWDKEKL 88 (130)
Q Consensus 56 ~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekL 88 (130)
=.+.|.-|++-.++++..|+--|...+||.-..
T Consensus 76 ~~edI~lv~~q~gvs~~~A~~AL~~~~gDl~~A 108 (115)
T PRK06369 76 PEEDIELVAEQTGVSEEEARKALEEANGDLAEA 108 (115)
T ss_pred CHHHHHHHHHHHCcCHHHHHHHHHHcCCcHHHH
Confidence 356678889999999999999999999997433
No 51
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=37.79 E-value=37 Score=20.82 Aligned_cols=23 Identities=13% Similarity=0.238 Sum_probs=19.4
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhC
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~f 81 (130)
.|.++.++|+++.-.|..||-||
T Consensus 12 tv~~~rd~lg~sRK~ai~lLE~l 34 (50)
T PF09107_consen 12 TVAEFRDLLGLSRKYAIPLLEYL 34 (50)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHH
T ss_pred cHHHHHHHHCccHHHHHHHHHHH
Confidence 46788899999999999999886
No 52
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=37.45 E-value=30 Score=23.01 Aligned_cols=27 Identities=19% Similarity=0.339 Sum_probs=22.2
Q ss_pred HHHHHHHhcCChhhHHHHcCCCCCCcce
Q psy7603 86 EKLMERYYDGDQESSTLDYSASTSSGLV 113 (130)
Q Consensus 86 ekLlE~y~e~D~~kvl~~aGl~~~~~~v 113 (130)
..+.++|.. ||+.++.+.||.+.+-.+
T Consensus 16 ~~~re~f~~-dp~a~~~~~~Lt~eE~~a 42 (77)
T cd07321 16 PEVKERFKA-DPEAVLAEYGLTPEEKAA 42 (77)
T ss_pred HHHHHHHHh-CHHHHHHHcCCCHHHHHH
Confidence 457899999 999999999998766433
No 53
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=37.23 E-value=92 Score=18.57 Aligned_cols=25 Identities=20% Similarity=0.145 Sum_probs=17.9
Q ss_pred CCCHHHHHHHHHhCCCChHHHHHHH
Q psy7603 68 EIPATTTRILLNHFKWDKEKLMERY 92 (130)
Q Consensus 68 ~vs~~~A~lLL~~fkWn~ekLlE~y 92 (130)
..+.......||.-+||+++-.+.+
T Consensus 28 ~~~d~~llRFLRARkf~v~~A~~mL 52 (55)
T PF03765_consen 28 DHDDNFLLRFLRARKFDVEKAFKML 52 (55)
T ss_dssp S-SHHHHHHHHHHTTT-HHHHHHHH
T ss_pred CCCHHHHHHHHHHccCCHHHHHHHH
Confidence 3456677888999999999877654
No 54
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=37.11 E-value=43 Score=19.00 Aligned_cols=22 Identities=18% Similarity=0.160 Sum_probs=16.4
Q ss_pred HHHHhhhhCCCHHHHHHHHHhC
Q psy7603 60 IKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~f 81 (130)
+.+|+.+|+|++...+.+.++.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 6788999999998776554433
No 55
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=36.95 E-value=44 Score=19.83 Aligned_cols=21 Identities=24% Similarity=0.498 Sum_probs=17.1
Q ss_pred HHHHhhhhCCCHHHHHHHHHh
Q psy7603 60 IKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~ 80 (130)
+.+|+..+++|++.+..+|+.
T Consensus 21 ~~eia~~~gl~~stv~r~L~t 41 (52)
T PF09339_consen 21 LSEIARALGLPKSTVHRLLQT 41 (52)
T ss_dssp HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 678899999999999888864
No 56
>PF06078 DUF937: Bacterial protein of unknown function (DUF937); InterPro: IPR009282 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 1Z67_A.
Probab=36.91 E-value=74 Score=22.78 Aligned_cols=34 Identities=15% Similarity=0.240 Sum_probs=27.0
Q ss_pred ecHHHHHHHH--HHHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 47 LSTEEIVQHM--IDCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 47 Ls~~eI~~~~--~e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
+.++.|...+ ...+++|+.-++|++..+.-||-.
T Consensus 90 ~g~~~l~~lfg~~~~~~~lA~~tGl~~~~~~~lL~~ 125 (137)
T PF06078_consen 90 IGPEILNSLFGGDDVIQQLAQQTGLSPDSAQQLLAM 125 (137)
T ss_dssp --HHHHHHHH--HHHHHHHHHHHT--HHHHHHHHHH
T ss_pred CCHHHHHHHhCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 4788888888 899999999999999999988853
No 57
>PRK12449 acyl carrier protein; Provisional
Probab=36.59 E-value=67 Score=20.54 Aligned_cols=58 Identities=17% Similarity=0.281 Sum_probs=38.8
Q ss_pred cHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCC
Q psy7603 48 STEEIVQHMIDCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTSS 110 (130)
Q Consensus 48 s~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~ 110 (130)
+.++|.+.+.+.+.++..+-...-.....|...++|+.-.+++-... +-...||..+.
T Consensus 2 ~~~~i~~~l~~il~~~~~~~~~~i~~~~~l~~dlg~DSl~~~~li~~-----lE~~f~i~i~~ 59 (80)
T PRK12449 2 TREEIFERLINLIQKQRSYLSLAITEQTHLKDDLAVDSIELVEFIIN-----VEDEFHIAIPD 59 (80)
T ss_pred CHHHHHHHHHHHHHHHhCCCccccCCCCcHHHHcCCcHHHHHHHHHH-----HHHHhCCCCCH
Confidence 56788888888877766554433334455668999999888776666 55556665443
No 58
>PF06059 DUF930: Domain of Unknown Function (DUF930); InterPro: IPR009273 This is a family of bacterial proteins with undetermined function. All bacteria in this family are from the Rhizobiales order.
Probab=36.47 E-value=17 Score=25.73 Aligned_cols=22 Identities=23% Similarity=0.561 Sum_probs=17.3
Q ss_pred CCCcceeeeeecccCCcccccc
Q psy7603 108 TSSGLVFSAVDFGSGGSWFEFK 129 (130)
Q Consensus 108 ~~~~~v~~~~~~~~~~~~~~~~ 129 (130)
..+.+.+..++|-|+|.|+.++
T Consensus 45 ~g~~l~a~gaAFRs~g~WY~l~ 66 (101)
T PF06059_consen 45 SGNVLDAPGAAFRSRGKWYDLS 66 (101)
T ss_pred cCCEEecCCcEEecCCeEEEEE
Confidence 4556668889999999998753
No 59
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=36.44 E-value=57 Score=25.04 Aligned_cols=49 Identities=14% Similarity=0.144 Sum_probs=37.1
Q ss_pred HHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCC
Q psy7603 60 IKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTSS 110 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~ 110 (130)
...+..|=||-|-.|+.||.+|.- +.|.+.-...|++.+..--||.++.
T Consensus 72 f~~L~~i~GIGpk~A~~il~~fg~--~~l~~~i~~~d~~~L~~v~Gig~k~ 120 (192)
T PRK00116 72 FRLLISVSGVGPKLALAILSGLSP--EELVQAIANGDVKALTKVPGIGKKT 120 (192)
T ss_pred HHHHhcCCCCCHHHHHHHHHhCCH--HHHHHHHHhCCHHHHHhCCCCCHHH
Confidence 556778999999999999999976 3455555555888887777875544
No 60
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=35.92 E-value=46 Score=18.63 Aligned_cols=22 Identities=14% Similarity=0.265 Sum_probs=17.4
Q ss_pred HHHHhhhhCCCHHHHHHHHHhC
Q psy7603 60 IKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~f 81 (130)
+.+++..+++++..+...|+.+
T Consensus 11 ~~~la~~l~~s~~tv~~~l~~L 32 (48)
T smart00419 11 RQEIAELLGLTRETVSRTLKRL 32 (48)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
Confidence 5678889999999888777653
No 61
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=34.86 E-value=50 Score=22.33 Aligned_cols=28 Identities=11% Similarity=0.019 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 53 VQHMIDCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 53 ~~~~~e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
-..+++...+|..-+|++++.|..++.+
T Consensus 9 D~~lK~~A~~vl~~lGls~S~Ai~~fl~ 36 (80)
T PRK11235 9 DDELKARAYAVLEKLGVTPSEALRLLLQ 36 (80)
T ss_pred CHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 3466788889999999999999777654
No 62
>PF13551 HTH_29: Winged helix-turn helix
Probab=34.35 E-value=37 Score=22.47 Aligned_cols=32 Identities=22% Similarity=0.280 Sum_probs=26.4
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCCh-HHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDK-EKLME 90 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~-ekLlE 90 (130)
.+.+|+..|++++....-+++.|+-.- +.|..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~ 46 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLP 46 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHh
Confidence 488999999999999999999888665 45554
No 63
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=34.25 E-value=55 Score=20.05 Aligned_cols=22 Identities=27% Similarity=0.315 Sum_probs=17.4
Q ss_pred HHHHhhhhCCCHHHHHHHHHhC
Q psy7603 60 IKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~f 81 (130)
|.+|+.+++||+..-+...+.+
T Consensus 3 i~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHHhc
Confidence 6789999999998877655544
No 64
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 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. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=33.86 E-value=1.1e+02 Score=18.31 Aligned_cols=35 Identities=23% Similarity=0.253 Sum_probs=27.7
Q ss_pred HHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 60 IKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
|.+|+..+||++......|.....=.+...++-..
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~ 36 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGPPRVSEETRERILE 36 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHH
Confidence 67899999999999999999886655666655544
No 65
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=33.48 E-value=88 Score=20.91 Aligned_cols=31 Identities=16% Similarity=0.417 Sum_probs=23.9
Q ss_pred HHHHHHhhhhC-CCHHHHHHHHHhCCCChHHH
Q psy7603 58 DCIKEVNNVVE-IPATTTRILLNHFKWDKEKL 88 (130)
Q Consensus 58 e~I~~V~~iL~-vs~~~A~lLL~~fkWn~ekL 88 (130)
+.++.+...-. ++-.++..||..|.++.+||
T Consensus 28 ~~l~~~~~~~~~~T~~Qv~~il~~f~fd~~kl 59 (95)
T PF14771_consen 28 KVLEAAAKTNNCFTCAQVKQILSLFSFDNDKL 59 (95)
T ss_pred HHHHHHHhcCCceeHHHHHHHHHHcCCCHHHH
Confidence 44555555555 89999999999999998775
No 66
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=33.35 E-value=54 Score=21.46 Aligned_cols=29 Identities=10% Similarity=0.181 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhhhhCCCHHHHHHHHHhCC
Q psy7603 54 QHMIDCIKEVNNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 54 ~~~~e~I~~V~~iL~vs~~~A~lLL~~fk 82 (130)
..+-..|++|+.-.+||...|.+|++=++
T Consensus 41 v~~Ga~~~el~~~CgL~~aEAeLl~~Lh~ 69 (70)
T PF10975_consen 41 VRQGASVEELMEECGLSRAEAELLLSLHR 69 (70)
T ss_pred HHcCCCHHHHHHHcCCCHHHHHHHHHHhc
Confidence 44556789999999999999999987543
No 67
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=32.95 E-value=57 Score=19.75 Aligned_cols=32 Identities=6% Similarity=0.102 Sum_probs=27.0
Q ss_pred ecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHH
Q psy7603 47 LSTEEIVQHMIDCIKEVNNVVEIPATTTRILL 78 (130)
Q Consensus 47 Ls~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL 78 (130)
.|+++..+......+.++.+|++++....+++
T Consensus 12 rt~eqK~~l~~~it~~l~~~lg~~~~~v~V~i 43 (63)
T TIGR00013 12 RTDEQKRQLIEGVTEAMAETLGANLESIVVII 43 (63)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCcccEEEEE
Confidence 57899999999999999999999987665544
No 68
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=32.91 E-value=63 Score=18.79 Aligned_cols=31 Identities=16% Similarity=0.369 Sum_probs=23.1
Q ss_pred HHHHHHHH--HHHHHhhhhCCCHHHHHHHHHhC
Q psy7603 51 EIVQHMID--CIKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 51 eI~~~~~e--~I~~V~~iL~vs~~~A~lLL~~f 81 (130)
.|...+.+ -+..|+..++|++.....++.+|
T Consensus 19 ~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 19 YILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34444443 48899999999999998887765
No 69
>PRK01905 DNA-binding protein Fis; Provisional
Probab=32.40 E-value=58 Score=21.29 Aligned_cols=32 Identities=16% Similarity=0.010 Sum_probs=24.6
Q ss_pred HHHHHHHH---HHHHHhhhhCCCHHHHHHHHHhCC
Q psy7603 51 EIVQHMID---CIKEVNNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 51 eI~~~~~e---~I~~V~~iL~vs~~~A~lLL~~fk 82 (130)
-|...+.. .+.+++..|+|++...+..|++|.
T Consensus 41 ~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~g 75 (77)
T PRK01905 41 LLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQHG 75 (77)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhC
Confidence 34444444 477899999999999999998874
No 70
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=31.58 E-value=1.1e+02 Score=18.64 Aligned_cols=28 Identities=7% Similarity=-0.045 Sum_probs=20.5
Q ss_pred HHHHHHHHHHhhhhCCCHHHHHHHHHhC
Q psy7603 54 QHMIDCIKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 54 ~~~~e~I~~V~~iL~vs~~~A~lLL~~f 81 (130)
..+...+.-++...++++..|.-+|++.
T Consensus 13 ~~I~~AkgiLm~~~g~~e~~A~~~Lr~~ 40 (56)
T PF03861_consen 13 RVIEQAKGILMARYGLSEDEAYRLLRRQ 40 (56)
T ss_dssp HHHHHHHHHHHHHHT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCcCHHHHHHHHHHH
Confidence 4566677778888999999999998863
No 71
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=31.35 E-value=48 Score=26.52 Aligned_cols=42 Identities=19% Similarity=0.249 Sum_probs=31.4
Q ss_pred ceEEecHHHHHHHHH--------HHHHHHhhhhCCCHHHHHHHHHhCCCCh
Q psy7603 43 VFEVLSTEEIVQHMI--------DCIKEVNNVVEIPATTTRILLNHFKWDK 85 (130)
Q Consensus 43 ~y~vLs~~eI~~~~~--------e~I~~V~~iL~vs~~~A~lLL~~fkWn~ 85 (130)
+-+-||.+++..+.. -.|..+++.+.|+|...+.+|+. ||--
T Consensus 7 p~k~Ls~~~~~~ir~L~~~~p~~~t~~~Lae~F~vspe~irrILks-kw~p 56 (225)
T PF06413_consen 7 PPKKLSREAMEQIRYLHKEDPEEWTVERLAESFKVSPEAIRRILKS-KWVP 56 (225)
T ss_pred CCCCCCHHHHHHHHHHHHhCccccCHHHHHhhCCCCHHHHHHHHhc-CCCC
Confidence 334577766655432 24788999999999999999876 8864
No 72
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=30.54 E-value=1.5e+02 Score=19.14 Aligned_cols=43 Identities=12% Similarity=0.239 Sum_probs=35.2
Q ss_pred HHHHHHHHHhhhhCC-CHHHHHHHHHhCCCChHHHHHHHhcCCh
Q psy7603 55 HMIDCIKEVNNVVEI-PATTTRILLNHFKWDKEKLMERYYDGDQ 97 (130)
Q Consensus 55 ~~~e~I~~V~~iL~v-s~~~A~lLL~~fkWn~ekLlE~y~e~D~ 97 (130)
...+.|+.|.+|++- |.......|+-.+-|-+...++....||
T Consensus 4 ~~rk~VQ~iKEiv~~hse~eIya~L~ecnMDpnea~qrLL~qD~ 47 (60)
T PF06972_consen 4 ASRKTVQSIKEIVGCHSEEEIYAMLKECNMDPNEAVQRLLSQDP 47 (60)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHhCCCHHHHHHHHHhcCc
Confidence 456778999999999 9999999999999999877777765343
No 73
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=30.52 E-value=63 Score=26.85 Aligned_cols=31 Identities=10% Similarity=0.238 Sum_probs=26.9
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCChHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDKEKLM 89 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLl 89 (130)
.+.+|++-|||+|.+.+-.-+.++|+.++-+
T Consensus 21 k~~dIAeklGvspntiksWKrr~gWs~~dev 51 (279)
T COG5484 21 KLKDIAEKLGVSPNTIKSWKRRDGWSATDEV 51 (279)
T ss_pred cHHHHHHHhCCChHHHHHHHHhcCCCchhhh
Confidence 4778999999999999999999999855444
No 74
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=30.24 E-value=28 Score=22.54 Aligned_cols=47 Identities=15% Similarity=0.212 Sum_probs=27.7
Q ss_pred HHHHHHHhCCCChHHHHHHHhc----CChhhHHHHcCCCCCCcceeeeeec
Q psy7603 73 TTRILLNHFKWDKEKLMERYYD----GDQESSTLDYSASTSSGLVFSAVDF 119 (130)
Q Consensus 73 ~A~lLL~~fkWn~ekLlE~y~e----~D~~kvl~~aGl~~~~~~v~~~~~~ 119 (130)
....|++.++|+...-+.+|.. ..-.+.|+++|+.+.....+...-|
T Consensus 17 ~ie~~~~~~~~~~~e~~~rf~~~L~~~Gv~~~L~~~G~~~GD~V~Ig~~eF 67 (69)
T PF09269_consen 17 KIERLVAMTNFDDEESLRRFQRKLKKMGVEKALRKAGAKEGDTVRIGDYEF 67 (69)
T ss_dssp HHHHHHTTEEE-TGGGHHHHHHHHHHTTHHHHHHTTT--TT-EEEETTEEE
T ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHHCCHHHHHHHcCCCCCCEEEEcCEEE
Confidence 3445677777776544444433 5668889999999888666655544
No 75
>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=30.01 E-value=78 Score=18.41 Aligned_cols=22 Identities=23% Similarity=0.357 Sum_probs=17.9
Q ss_pred HHHHHHhhhhCCCHHHHHHHHH
Q psy7603 58 DCIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~ 79 (130)
....+|+..|++|...++.+++
T Consensus 21 ~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 21 LTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp -SHHHHHHHHTSCHHHHHHHHH
T ss_pred CCHHHHHHHHCCcHHHHHHHHH
Confidence 4578899999999999887765
No 76
>PF07746 LigA: Aromatic-ring-opening dioxygenase LigAB, LigA subunit; InterPro: IPR011986 Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes (IPR000627 from INTERPRO) use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [, ]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues. Extradiol dioxygenases are usually homo-multimeric, bind one atom of ferrous ion per subunit and have a subunit size of about 33 kDa. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes (IPR000486 from INTERPRO) show sequence similarity, with the two-domain class II enzymes having evolved from a class I enzyme through gene duplication. Class III enzymes are different in sequence and structure, but they do share several common active-site characteristics with the class II enzymes, in particular the coordination sphere and the disposition of the putative catalytic base are very similar. Class III enzymes usually have two subunits, designated A (IPR004183 from INTERPRO) and B (IPR004183 from INTERPRO). LigAB is a protocatechuate 4,5-dioxygenase (1.13.11.8 from EC) that belongs to the extradiol class III enzyme family. The LigA subunit of this enzyme is multi-helical, containing a compact array of 6 short helices [].; PDB: 1BOU_A 1B4U_A.
Probab=29.92 E-value=31 Score=23.70 Aligned_cols=32 Identities=16% Similarity=0.241 Sum_probs=22.9
Q ss_pred HHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCCc
Q psy7603 77 LLNHFKWDKEKLMERYYDGDQESSTLDYSASTSSG 111 (130)
Q Consensus 77 LL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~~ 111 (130)
+++.+ +.....++|-. ||+.++.+.||.+.+-
T Consensus 4 f~~~L--~~~~~r~~F~~-D~~a~~~~~~Lt~eer 35 (88)
T PF07746_consen 4 FCWSL--NDPENRERFLA-DPEAYLDEYGLTEEER 35 (88)
T ss_dssp HHHGG--GSHHHHHHHHH--HHHHHHCCT--HHHH
T ss_pred HHHHH--cCHHHHHHHHH-CHHHHHHHcCCCHHHH
Confidence 44455 66778899999 9999999999977653
No 77
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=29.89 E-value=59 Score=23.41 Aligned_cols=23 Identities=4% Similarity=0.042 Sum_probs=18.9
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+.+|+.+|+||+..++..|+.
T Consensus 129 ~s~~eIA~~lgis~~tV~~~l~R 151 (164)
T PRK12547 129 FSYEDAAAICGCAVGTIKSRVSR 151 (164)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Confidence 34688999999999999887764
No 78
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=29.84 E-value=1.2e+02 Score=18.56 Aligned_cols=30 Identities=17% Similarity=0.233 Sum_probs=23.4
Q ss_pred EEecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 45 EVLSTEEIVQHMIDCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 45 ~vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+|+++|.+.+.+....+ .|.....|+++
T Consensus 13 ~~MS~eEI~~er~eL~~~L------dP~li~~L~~R 42 (49)
T PF08621_consen 13 ASMSPEEIEEEREELLESL------DPKLIEFLKKR 42 (49)
T ss_pred HhCCHHHHHHHHHHHHHhC------CHHHHHHHHHh
Confidence 4689999999999887754 77777777664
No 79
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=29.75 E-value=49 Score=23.49 Aligned_cols=34 Identities=15% Similarity=0.277 Sum_probs=26.3
Q ss_pred cceEEecHHHHHHHHHHHHHHHhhhhCCCHHHHH
Q psy7603 42 FVFEVLSTEEIVQHMIDCIKEVNNVVEIPATTTR 75 (130)
Q Consensus 42 ~~y~vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~ 75 (130)
..++.++.+.|...=...|+++++|+++|++.-.
T Consensus 4 lr~rGi~~e~v~~~S~~LideLa~i~~~p~e~ft 37 (108)
T PF08921_consen 4 LRFRGIEEEQVQELSKELIDELAEICGCPRENFT 37 (108)
T ss_dssp EEEESS-HHHHHHHHHHHHHHHHHHHT--GGG-E
T ss_pred EEEecCCHHHHHHHhHHHHHHHHHHHCCCcceEE
Confidence 4578899999999999999999999999986543
No 80
>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=29.46 E-value=63 Score=21.53 Aligned_cols=24 Identities=17% Similarity=0.069 Sum_probs=20.1
Q ss_pred HHHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 57 IDCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 57 ~e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.-.+.+|+.+|+||+..++.+++.
T Consensus 32 GlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 32 GKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhc
Confidence 335789999999999999988773
No 81
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=28.86 E-value=64 Score=22.73 Aligned_cols=22 Identities=5% Similarity=0.052 Sum_probs=18.3
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.+.+|+.+||||+..++..|..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~r 145 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSR 145 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999877764
No 82
>PHA03101 DNA topoisomerase type I; Provisional
Probab=28.79 E-value=77 Score=26.81 Aligned_cols=28 Identities=14% Similarity=0.166 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHhhhhCCCHHHHHH
Q psy7603 49 TEEIVQHMIDCIKEVNNVVEIPATTTRI 76 (130)
Q Consensus 49 ~~eI~~~~~e~I~~V~~iL~vs~~~A~l 76 (130)
..++.+.+...|.+|++.||-+|.+|+-
T Consensus 246 ~~~~kk~i~~~i~~vA~~LGNTPaV~R~ 273 (314)
T PHA03101 246 LPSIKKLISLSIKQTAEIVGHTPSISKS 273 (314)
T ss_pred hhHHHHHHHHHHHHHHHHhCCCHhhHHh
Confidence 3557778999999999999999999984
No 83
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.69 E-value=63 Score=23.70 Aligned_cols=21 Identities=14% Similarity=0.313 Sum_probs=17.8
Q ss_pred HHHHHhhhhCCCHHHHHHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~ 79 (130)
.+++|+.+|+||++.++..|+
T Consensus 145 s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467899999999999987776
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=28.66 E-value=74 Score=19.88 Aligned_cols=21 Identities=14% Similarity=0.314 Sum_probs=16.9
Q ss_pred HHHHhhhhCCCHHHHHHHHHh
Q psy7603 60 IKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+|+..|+|+|..+.-.|++
T Consensus 25 ~~~iA~~L~vs~~tvt~ml~~ 45 (60)
T PF01325_consen 25 TKDIAERLGVSPPTVTEMLKR 45 (60)
T ss_dssp HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHCCChHHHHHHHHH
Confidence 568899999999999887765
No 85
>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=28.52 E-value=66 Score=22.30 Aligned_cols=22 Identities=18% Similarity=0.277 Sum_probs=18.0
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.+.+|+.+||+|+...+..|+.
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~r 152 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISK 152 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 5678899999999988877764
No 86
>PRK10244 anti-RssB factor; Provisional
Probab=27.70 E-value=77 Score=22.03 Aligned_cols=32 Identities=22% Similarity=0.409 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHH-hhhhCCCHHHHHHHHHhCC
Q psy7603 51 EIVQHMIDCIKEV-NNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 51 eI~~~~~e~I~~V-~~iL~vs~~~A~lLL~~fk 82 (130)
.+...+...|..+ ..--+++.+.+.+||.||+
T Consensus 47 ~li~~Ie~Ai~~a~~~~~~~~~~D~eLL~~~v~ 79 (88)
T PRK10244 47 ELIEQVEGAINAVSKPDDSVPDSDTELLLTYVN 79 (88)
T ss_pred HHHHHHHHHHHHhccccccccchHHHHHHHHHH
Confidence 3444444455555 4555788899999999875
No 87
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=27.22 E-value=1.1e+02 Score=18.34 Aligned_cols=33 Identities=9% Similarity=0.189 Sum_probs=27.0
Q ss_pred ecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHH
Q psy7603 47 LSTEEIVQHMIDCIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 47 Ls~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~ 79 (130)
.|+++..+......+.+..+|++++....+++.
T Consensus 12 rs~eqk~~l~~~it~~l~~~~~~p~~~v~V~i~ 44 (62)
T PRK00745 12 RTVEQKRKLVEEITRVTVETLGCPPESVDIIIT 44 (62)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCChhHEEEEEE
Confidence 578888888888888899999999977665543
No 88
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=26.83 E-value=63 Score=18.47 Aligned_cols=16 Identities=31% Similarity=0.474 Sum_probs=12.3
Q ss_pred HHHHhhhhCCCHHHHH
Q psy7603 60 IKEVNNVVEIPATTTR 75 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~ 75 (130)
|.+|+.+++|++..-|
T Consensus 2 i~e~A~~~gvs~~tlR 17 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLR 17 (38)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCCCHHHHH
Confidence 6789999999987655
No 89
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=26.80 E-value=89 Score=17.99 Aligned_cols=20 Identities=25% Similarity=0.300 Sum_probs=14.1
Q ss_pred HHHHhhhhCCCHHHHHHHHH
Q psy7603 60 IKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~ 79 (130)
+.+++..+++++..++..|+
T Consensus 23 ~~~la~~~~vs~~tv~~~l~ 42 (60)
T smart00345 23 ERELAAQLGVSRTTVREALS 42 (60)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 55677778888877765554
No 90
>CHL00098 tsf elongation factor Ts
Probab=26.63 E-value=2.8e+02 Score=21.73 Aligned_cols=59 Identities=20% Similarity=0.176 Sum_probs=45.7
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhcCChhhHHHHcCCCCCCcceeee
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYDGDQESSTLDYSASTSSGLVFSA 116 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl~~aGl~~~~~~v~~~ 116 (130)
+.|.++.+.++.+--.|+-=|...+||.++.++-.....-.+.-+++|=....+.|.+-
T Consensus 3 ~~ik~LR~~Tgag~~dck~AL~e~~gd~~~A~~~Lr~~g~~~a~kk~~r~~~eG~V~~y 61 (200)
T CHL00098 3 ELVKELRDKTGAGMMDCKKALQEANGDFEKALESLRQKGLASANKKSTRITTEGLIESY 61 (200)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHhhhhHHHHhhccccccCeEEEE
Confidence 46889999999999999999999999999998766663445555666656666666443
No 91
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=26.59 E-value=1.1e+02 Score=20.35 Aligned_cols=33 Identities=6% Similarity=0.212 Sum_probs=26.0
Q ss_pred CCChHHHHHHHhcCChhhHHHHcCCCCCCcceee
Q psy7603 82 KWDKEKLMERYYDGDQESSTLDYSASTSSGLVFS 115 (130)
Q Consensus 82 kWn~ekLlE~y~e~D~~kvl~~aGl~~~~~~v~~ 115 (130)
-|.-.....+... ||..+|.+.|+..|.+..+-
T Consensus 13 Aw~Dp~Fr~~Ll~-DPraaL~e~G~~~P~~~~i~ 45 (77)
T TIGR03793 13 AWEDEAFKQALLT-NPKEALEREGVQVPAEVEVK 45 (77)
T ss_pred HHcCHHHHHHHHH-CHHHHHHHhCCCCCCceEEE
Confidence 3666677777777 99999999999988866543
No 92
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=26.58 E-value=83 Score=21.07 Aligned_cols=28 Identities=7% Similarity=0.005 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 53 VQHMIDCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 53 ~~~~~e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
-..+++....|..-+|++++.|..++.+
T Consensus 10 d~~lK~~a~~i~~~lGl~~s~ai~~fl~ 37 (83)
T TIGR02384 10 DEELKKEAYAVFEELGLTPSTAIRMFLK 37 (83)
T ss_pred CHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 3456777888889999999999766543
No 93
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=26.54 E-value=92 Score=17.64 Aligned_cols=22 Identities=23% Similarity=0.374 Sum_probs=17.5
Q ss_pred HHHHHHhhhhCCCHHHHHHHHH
Q psy7603 58 DCIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~ 79 (130)
....+|+..+++++...+..++
T Consensus 16 ~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 16 KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 3567888999999988887765
No 94
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=26.47 E-value=80 Score=17.67 Aligned_cols=22 Identities=23% Similarity=0.376 Sum_probs=17.0
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.+.+++..|++++..++..|..
T Consensus 16 s~~~l~~~l~~s~~tv~~~l~~ 37 (53)
T smart00420 16 SVEELAELLGVSEMTIRRDLNK 37 (53)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4677888889999988776654
No 95
>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=26.40 E-value=73 Score=23.06 Aligned_cols=23 Identities=9% Similarity=0.137 Sum_probs=18.4
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
....+|+.+||||++..+..|+.
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 151 LTVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Confidence 34678999999999998877764
No 96
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=26.40 E-value=82 Score=19.30 Aligned_cols=32 Identities=13% Similarity=0.157 Sum_probs=26.0
Q ss_pred EecHHHHHHHHHHHHHHHhhhhCCCHHHHHHH
Q psy7603 46 VLSTEEIVQHMIDCIKEVNNVVEIPATTTRIL 77 (130)
Q Consensus 46 vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~lL 77 (130)
-.|.++..+......+-+..++++|+....++
T Consensus 11 Grs~EqK~~L~~~it~a~~~~~~~p~~~v~V~ 42 (60)
T PRK02289 11 GRSQEQKNALAREVTEVVSRIAKAPKEAIHVF 42 (60)
T ss_pred CCCHHHHHHHHHHHHHHHHHHhCcCcceEEEE
Confidence 35889999999999999999999987654443
No 97
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=26.38 E-value=1.1e+02 Score=22.41 Aligned_cols=32 Identities=19% Similarity=0.306 Sum_probs=24.5
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
.+++|+.-.||+++ .|.+||+ ||+.|+..-..
T Consensus 30 s~~~IA~~agvs~~---~lY~hF~-sKe~L~~av~~ 61 (202)
T TIGR03613 30 SLEQIAELAGVSKT---NLLYYFP-SKDALYLAVLR 61 (202)
T ss_pred CHHHHHHHhCCCHH---HHHHHcC-CHHHHHHHHHH
Confidence 36778888899885 4778998 88887766655
No 98
>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=26.04 E-value=93 Score=19.31 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=17.9
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.+.+|+..|+|++....--||.
T Consensus 25 tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 25 TLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 3678999999999988777664
No 99
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=25.92 E-value=85 Score=21.57 Aligned_cols=24 Identities=17% Similarity=0.123 Sum_probs=21.0
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCC
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fk 82 (130)
.+.+++.+|||++...+..|++|+
T Consensus 70 n~s~AAr~LGIsRsTL~rKLkr~g 93 (95)
T PRK00430 70 NQTRAALMLGINRGTLRKKLKKYG 93 (95)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHhC
Confidence 478889999999999999998875
No 100
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.72 E-value=74 Score=22.85 Aligned_cols=22 Identities=18% Similarity=0.246 Sum_probs=17.2
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.+.+|+.+||+|++.++..|+.
T Consensus 136 s~~EIA~~lgis~~tV~~~l~r 157 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHY 157 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4578899999999888776654
No 101
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=25.41 E-value=82 Score=18.85 Aligned_cols=22 Identities=14% Similarity=0.200 Sum_probs=17.0
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.+.++++.+++++..+..+|+.
T Consensus 27 s~~ela~~~g~s~~tv~r~l~~ 48 (67)
T cd00092 27 TRQEIADYLGLTRETVSRTLKE 48 (67)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 3567888899999888776654
No 102
>PF06385 Baculo_LEF-11: Baculovirus LEF-11 protein; InterPro: IPR009429 This family consists of several Baculovirus LEF-11 proteins. The exact function of this family is unknown although it has been shown that LEF-11 is required for viral DNA replication during the infection cycle [] and plays a role in late/very late gene activation.; GO: 0006355 regulation of transcription, DNA-dependent, 0019058 viral infectious cycle
Probab=25.34 E-value=84 Score=22.06 Aligned_cols=27 Identities=11% Similarity=0.199 Sum_probs=24.4
Q ss_pred EecHHHHHHHHHHHHHHHhhhhCCCHH
Q psy7603 46 VLSTEEIVQHMIDCIKEVNNVVEIPAT 72 (130)
Q Consensus 46 vLs~~eI~~~~~e~I~~V~~iL~vs~~ 72 (130)
|||.+||.+.+.+.|+......++..-
T Consensus 1 cLTRSevYAlvrE~IN~~K~~~d~~nV 27 (94)
T PF06385_consen 1 CLTRSEVYALVREVINKRKHTNDTENV 27 (94)
T ss_pred CCcHHHHHHHHHHHHHHhhccCcchhH
Confidence 799999999999999999988888773
No 103
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.11 E-value=81 Score=22.34 Aligned_cols=23 Identities=17% Similarity=0.187 Sum_probs=17.8
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
-...+|+.+||+|++..+..|..
T Consensus 123 ~s~~EIA~~lgis~~tV~~~l~R 145 (160)
T PRK09642 123 KSYQEIALQEKIEVKTVEMKLYR 145 (160)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 44678899999999888776653
No 104
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=25.04 E-value=98 Score=18.19 Aligned_cols=20 Identities=25% Similarity=0.303 Sum_probs=11.9
Q ss_pred HHHHhhhhCCCHHHHHHHHH
Q psy7603 60 IKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~ 79 (130)
+++++..++|++..++..|.
T Consensus 28 ~~~la~~~~is~~~v~~~l~ 47 (66)
T cd07377 28 ERELAEELGVSRTTVREALR 47 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 44566666777666664443
No 105
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=24.89 E-value=96 Score=18.95 Aligned_cols=21 Identities=29% Similarity=0.330 Sum_probs=17.6
Q ss_pred HHHHHhhhhCCCHHHHHHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~ 79 (130)
.+.++++.|+||+..+|.=|.
T Consensus 16 s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred EHHHHHHHHCcCHHHHHHHHH
Confidence 478999999999999986554
No 106
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=24.81 E-value=99 Score=19.10 Aligned_cols=23 Identities=17% Similarity=0.190 Sum_probs=18.8
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+.+|+..+++|.+.+...|+.
T Consensus 23 ~t~~eIa~~l~i~~~~v~~~L~~ 45 (68)
T PF01978_consen 23 ATAEEIAEELGISRSTVYRALKS 45 (68)
T ss_dssp EEHHHHHHHHTSSHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 34789999999999999877653
No 107
>KOG3890|consensus
Probab=24.66 E-value=57 Score=27.98 Aligned_cols=32 Identities=6% Similarity=0.335 Sum_probs=29.4
Q ss_pred ccceEEecHHHHHHHHHHHHHHHhhhhCCCHH
Q psy7603 41 EFVFEVLSTEEIVQHMIDCIKEVNNVVEIPAT 72 (130)
Q Consensus 41 ~~~y~vLs~~eI~~~~~e~I~~V~~iL~vs~~ 72 (130)
...|+.+|.++|+......+++...+|++||-
T Consensus 72 ~~~~klMt~eqLe~~~~~~ve~A~~~LqmpPV 103 (391)
T KOG3890|consen 72 SSETKLMTNEQLENEFQNLVERAQQILQMPPV 103 (391)
T ss_pred CchhhhhhHHHHHHHHHHHHHHHHHHhcCCCc
Confidence 44889999999999999999999999999983
No 108
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.64 E-value=81 Score=23.38 Aligned_cols=23 Identities=13% Similarity=0.242 Sum_probs=18.3
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+.+|+.+|++|++..+..|+.
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~R 173 (189)
T PRK12530 151 LSSEQICQECDISTSNLHVLLYR 173 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 34678999999999998776653
No 109
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=24.51 E-value=1.1e+02 Score=18.87 Aligned_cols=18 Identities=33% Similarity=0.540 Sum_probs=15.0
Q ss_pred HHHHhhhhCCCHHHHHHH
Q psy7603 60 IKEVNNVVEIPATTTRIL 77 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lL 77 (130)
|.+|+.+++|++...+..
T Consensus 3 i~evA~~~gvs~~tlR~~ 20 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYY 20 (67)
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 678999999999887744
No 110
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=24.37 E-value=1.1e+02 Score=22.38 Aligned_cols=33 Identities=12% Similarity=0.237 Sum_probs=25.1
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
-.|.+|+.-.||+++ .|.+||+ +|+.|+..-+.
T Consensus 29 tSi~~Ia~~aGvsk~---~lY~~F~-sK~~L~~~~~~ 61 (192)
T PRK14996 29 MTVRRIASEAQVAAG---QVHHHFS-SAGELKALAFI 61 (192)
T ss_pred ccHHHHHHHhCCCcH---HHHHHcC-CHHHHHHHHHH
Confidence 357788888999875 4889998 99998655433
No 111
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=24.30 E-value=1e+02 Score=18.11 Aligned_cols=32 Identities=13% Similarity=0.269 Sum_probs=24.9
Q ss_pred ecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHH
Q psy7603 47 LSTEEIVQHMIDCIKEVNNVVEIPATTTRILL 78 (130)
Q Consensus 47 Ls~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL 78 (130)
.++++..+......+-+..++++++....+++
T Consensus 11 rt~eqk~~l~~~i~~~l~~~~g~~~~~v~V~i 42 (58)
T cd00491 11 RTDEQKRELIERVTEAVSEILGAPEATIVVII 42 (58)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCcccEEEEE
Confidence 46888888888888888899999887554443
No 112
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 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 (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=24.26 E-value=81 Score=23.26 Aligned_cols=23 Identities=22% Similarity=0.254 Sum_probs=19.3
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
-...+|+.+||||+..++..|+.
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~R 170 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHR 170 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 45688999999999999888765
No 113
>PRK08402 replication factor A; Reviewed
Probab=24.23 E-value=1.1e+02 Score=25.97 Aligned_cols=28 Identities=32% Similarity=0.479 Sum_probs=19.4
Q ss_pred ecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHH
Q psy7603 47 LSTEEIVQHMIDCIKEVNNVVEIPATTTRILL 78 (130)
Q Consensus 47 Ls~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL 78 (130)
++.++|+..+.+.|++ .+|++..|..||
T Consensus 19 vs~eei~~~l~~lv~~----~~~~e~~A~~~i 46 (355)
T PRK08402 19 MSREEIEEKIREIMKE----EGISEHAAALLL 46 (355)
T ss_pred CCHHHHHHHHHHHHHH----cCCCHHHHHHHH
Confidence 6677777777776666 458887775554
No 114
>PRK13778 paaA phenylacetate-CoA oxygenase subunit PaaA; Provisional
Probab=24.00 E-value=2.9e+02 Score=23.34 Aligned_cols=63 Identities=8% Similarity=0.106 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHhhhhCCCHHHH----HHHHHhCC-CChHHHHHHHhcCChhhHHHHcCCCCCC-cceee
Q psy7603 52 IVQHMIDCIKEVNNVVEIPATTT----RILLNHFK-WDKEKLMERYYDGDQESSTLDYSASTSS-GLVFS 115 (130)
Q Consensus 52 I~~~~~e~I~~V~~iL~vs~~~A----~lLL~~fk-Wn~ekLlE~y~e~D~~kvl~~aGl~~~~-~~v~~ 115 (130)
++..++..---+..+|+.++... ..+=...+ ++-+.|-++|.. .-..++..+||..|. .+.|+
T Consensus 192 ~Q~Ald~~Wp~~~emFg~~d~~s~~~~~~~~~Gik~~~n~eLR~~w~~-~v~~~l~~~gL~vP~~~~~~~ 260 (314)
T PRK13778 192 AQDALNRWWWPALMMFGPPDDDSPHSAQSMAWKIKRFSNDELRQKFVD-ATVPQAEVLGLTLPDPDLRWN 260 (314)
T ss_pred HHHHHHHHHHHHHhhcCCCcchhhhHHHHHHhCCCCCCHHHHHHHHHH-HHHHHHHHcCCCCCCCcCCcc
Confidence 44444444445678888887544 22333455 889999999999 999999999998875 34443
No 115
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=23.60 E-value=91 Score=20.59 Aligned_cols=27 Identities=0% Similarity=0.052 Sum_probs=19.2
Q ss_pred HHHHHHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 54 QHMIDCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 54 ~~~~e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+++....|..-+|++++.|..++.+
T Consensus 10 ~~lK~~a~~il~~~Glt~s~ai~~fl~ 36 (83)
T PF04221_consen 10 EELKEEAEAILEELGLTLSDAINMFLK 36 (83)
T ss_dssp HHHHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 356677888999999999999766543
No 116
>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=23.60 E-value=82 Score=18.29 Aligned_cols=31 Identities=26% Similarity=0.259 Sum_probs=20.9
Q ss_pred HHHHHHHHH--HHHHHHhhhhCCCHHHHHHHHH
Q psy7603 49 TEEIVQHMI--DCIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 49 ~~eI~~~~~--e~I~~V~~iL~vs~~~A~lLL~ 79 (130)
.++|.++.. .-|.+|+..++|+.......|.
T Consensus 11 ~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 355555554 3689999999999988776664
No 117
>smart00741 SapB Saposin (B) Domains. Present in multiple copies in prosaposin and in pulmonary surfactant-associated protein B. In plant aspartic proteinases, a saposin domain is circularly permuted. This causes the prediction algorithm to predict two such domains, where only one is truly present.
Probab=23.54 E-value=1.7e+02 Score=17.41 Aligned_cols=51 Identities=4% Similarity=0.130 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHhhhhC-CCHHHHHHHHHhCCCChHHHHHHHhc-CChhhHHHHcCC
Q psy7603 53 VQHMIDCIKEVNNVVE-IPATTTRILLNHFKWDKEKLMERYYD-GDQESSTLDYSA 106 (130)
Q Consensus 53 ~~~~~e~I~~V~~iL~-vs~~~A~lLL~~fkWn~ekLlE~y~e-~D~~kvl~~aGl 106 (130)
...+.+.+.++...++ -....+..++..|- ..++..+.. .+|..++...|+
T Consensus 23 ~~~i~~~~~~~C~~~~~~~~~~C~~~v~~~~---~~ii~~i~~~~~p~~iC~~l~~ 75 (76)
T smart00741 23 EEEIKKALEKVCKKLPKSLSDQCKEFVDQYG---PEIIDLLEQGLDPKDVCQKLGL 75 (76)
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHHHHHHHHH---HHHHHHHHhCCCHHHHHHHcCC
Confidence 4566677888888888 56677888887775 455555544 348888887765
No 118
>TIGR02156 PA_CoA_Oxy1 phenylacetate-CoA oxygenase, PaaG subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=23.50 E-value=3.1e+02 Score=22.82 Aligned_cols=59 Identities=5% Similarity=-0.037 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHhhhhCCCHHHHHH--HHH--hCC-CChHHHHHHHhcCChhhHHHHcCCCCCCc
Q psy7603 52 IVQHMIDCIKEVNNVVEIPATTTRI--LLN--HFK-WDKEKLMERYYDGDQESSTLDYSASTSSG 111 (130)
Q Consensus 52 I~~~~~e~I~~V~~iL~vs~~~A~l--LL~--~fk-Wn~ekLlE~y~e~D~~kvl~~aGl~~~~~ 111 (130)
++..++..---+..+|+.++..... .|. ..+ ++-+.|-++|.. ....+|.++||..|.+
T Consensus 174 ~Q~Ald~~Wp~~~emFg~~d~e~~~~~~~~~~Gi~~~~n~eLR~~w~~-~v~~~l~~agL~~P~~ 237 (289)
T TIGR02156 174 AQDALNRWWWPSLMMFGPHDADSPNSGQSTKWKIKRNSNDELRQKFID-ATVPQLESLGLTIPDP 237 (289)
T ss_pred HHHHHHHHHHHHHhhcCCCchhhhhHHHHHhCCCCCCCHHHHHHHHHH-HHHHHHHHcCCCCCCC
Confidence 4444444444567778888754422 223 555 788999999999 9999999999988763
No 119
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=23.17 E-value=1.4e+02 Score=17.81 Aligned_cols=24 Identities=4% Similarity=0.163 Sum_probs=16.9
Q ss_pred HHHHHHHHHhhhhCCCHHHHHHHH
Q psy7603 55 HMIDCIKEVNNVVEIPATTTRILL 78 (130)
Q Consensus 55 ~~~e~I~~V~~iL~vs~~~A~lLL 78 (130)
.....+.=|+.+|+++|...+.++
T Consensus 23 ~~~~llpvi~tlL~fs~~e~~~i~ 46 (46)
T PF01465_consen 23 EREQLLPVIATLLKFSPEEKQKIL 46 (46)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHH
T ss_pred hHHHHHHHHHHHHCCCHHHHHhhC
Confidence 455667889999999999988764
No 120
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.87 E-value=1.2e+02 Score=16.97 Aligned_cols=21 Identities=24% Similarity=0.292 Sum_probs=16.9
Q ss_pred HHHHHhhhhCCCHHHHHHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~ 79 (130)
...+|+..|+|++...+..++
T Consensus 20 s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 20 TNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 467888999999988877665
No 121
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=22.83 E-value=63 Score=23.24 Aligned_cols=22 Identities=18% Similarity=0.403 Sum_probs=19.5
Q ss_pred HHHHHHhhhhCCCHHHHHHHHH
Q psy7603 58 DCIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~ 79 (130)
.-|.+|+..|++|.+.+++||-
T Consensus 56 ~SVAEiAA~L~lPlgVvrVLvs 77 (114)
T PF05331_consen 56 LSVAEIAARLGLPLGVVRVLVS 77 (114)
T ss_pred ccHHHHHHhhCCCchhhhhhHH
Confidence 4588999999999999999984
No 122
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=22.75 E-value=1.9e+02 Score=17.49 Aligned_cols=34 Identities=9% Similarity=0.133 Sum_probs=25.9
Q ss_pred cceEEecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHH
Q psy7603 42 FVFEVLSTEEIVQHMIDCIKEVNNVVEIPATTTRILL 78 (130)
Q Consensus 42 ~~y~vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL 78 (130)
..++.++.++|. +...|..+.. .|+|...++.||
T Consensus 34 ~~~r~yt~~~v~--~l~~i~~l~~-~g~~l~~i~~~~ 67 (68)
T cd01104 34 GGHRLYSEADVA--RLRLIRRLTS-EGVRISQAAALA 67 (68)
T ss_pred CCCeecCHHHHH--HHHHHHHHHH-CCCCHHHHHHHh
Confidence 467889999996 3445666666 899999888776
No 123
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=22.75 E-value=89 Score=21.89 Aligned_cols=29 Identities=14% Similarity=0.128 Sum_probs=23.8
Q ss_pred ChHHHHHHHhcCChhhHHHHcCCCCCCcce
Q psy7603 84 DKEKLMERYYDGDQESSTLDYSASTSSGLV 113 (130)
Q Consensus 84 n~ekLlE~y~e~D~~kvl~~aGl~~~~~~v 113 (130)
+.-..-++|-. ||+.++.++||.+.+-..
T Consensus 16 ~~a~~RerF~~-D~ea~~~e~gLt~Ee~~a 44 (94)
T cd07923 16 IEPAHRERFLE-DPEALFDEAGLTEEERTL 44 (94)
T ss_pred CCHHHHHHHHh-CHHHHHHHcCCCHHHHHH
Confidence 35678899999 999999999998766443
No 124
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=22.69 E-value=92 Score=16.99 Aligned_cols=26 Identities=19% Similarity=0.248 Sum_probs=20.1
Q ss_pred HHHHHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 55 HMIDCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 55 ~~~e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.....++++..+=+|.|..|..+|.+
T Consensus 5 ~~pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 5 LIPASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp HHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred cCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence 44556788999999999999988864
No 125
>PF02561 FliS: Flagellar protein FliS; InterPro: IPR003713 The fliD operon of several bacteria consists of three flagellar genes, fliD, fliS, and fliT, and is transcribed in this order []. In Bacillus subtilis the operon encoding the flagellar proteins FliD, FliS, and FliT is sigma D-dependent [].; GO: 0009296 flagellum assembly, 0009288 bacterial-type flagellum; PDB: 1VH6_A 3IQC_B 3K1I_B 1ORJ_B 1ORY_A.
Probab=22.49 E-value=1.6e+02 Score=20.58 Aligned_cols=49 Identities=16% Similarity=0.273 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHhhhhCCC--HHHHHHHHHhCCCChHHHHHHHhcCChhhHH
Q psy7603 53 VQHMIDCIKEVNNVVEIP--ATTTRILLNHFKWDKEKLMERYYDGDQESST 101 (130)
Q Consensus 53 ~~~~~e~I~~V~~iL~vs--~~~A~lLL~~fkWn~ekLlE~y~e~D~~kvl 101 (130)
......+|.++...|+.. ...|.-|-+-|.|-..+|.+....+|++.+-
T Consensus 52 l~ka~~Ii~~L~~~Ld~e~g~eia~~L~~lY~y~~~~L~~A~~~~d~~~l~ 102 (122)
T PF02561_consen 52 LQKAQDIITELQSSLDFEKGGEIADNLFRLYDYMIRQLVQANLKKDPERLD 102 (122)
T ss_dssp HHHHHHHHHHHHHTCCTTTTHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH
T ss_pred HHHHHHHHHHHHhhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHhCCHHHHH
Confidence 345566788999999998 8899999999999999999998886665543
No 126
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=22.43 E-value=70 Score=19.86 Aligned_cols=21 Identities=14% Similarity=0.403 Sum_probs=16.2
Q ss_pred HHHhhhhCCCHHHHHHHHHhC
Q psy7603 61 KEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 61 ~~V~~iL~vs~~~A~lLL~~f 81 (130)
+++++++++++......|+++
T Consensus 32 ~~iA~~~g~sr~tv~r~l~~l 52 (76)
T PF13545_consen 32 EEIADMLGVSRETVSRILKRL 52 (76)
T ss_dssp HHHHHHHTSCHHHHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHHHH
Confidence 446788999998888777764
No 127
>PF01028 Topoisom_I: Eukaryotic DNA topoisomerase I, catalytic core; InterPro: IPR013500 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the catalytic core of eukaryotic and viral topoisomerase I (type IB) enzymes, which occurs near the C-terminal region of the protein. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity []. The crystal structures of human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes []. Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. The crystal structure of an amino-terminal fragment of vaccinia virus DNA topoisomerase I shows that the fragment forms a five-stranded, antiparallel beta-sheet with two short alpha-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure []. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2F4Q_A 3M4A_A 3IGC_A 2H7G_X 2H7F_X 1A41_A 1VCC_A 1TL8_A 1K4T_A 1A36_A ....
Probab=22.37 E-value=1.3e+02 Score=24.22 Aligned_cols=30 Identities=20% Similarity=0.168 Sum_probs=27.0
Q ss_pred ecHHHHHHHHHHHHHHHhhhhCCCHHHHHH
Q psy7603 47 LSTEEIVQHMIDCIKEVNNVVEIPATTTRI 76 (130)
Q Consensus 47 Ls~~eI~~~~~e~I~~V~~iL~vs~~~A~l 76 (130)
.+..+....+...+.+|+..||=+|.+|+-
T Consensus 177 ~~~~~~~~~~~~a~~~VA~~LgnTpaV~r~ 206 (234)
T PF01028_consen 177 ESEKERKKAYNAAVKEVAELLGNTPAVCRK 206 (234)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHTSEHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCccccch
Confidence 467778889999999999999999999984
No 128
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=22.26 E-value=1e+02 Score=21.50 Aligned_cols=23 Identities=13% Similarity=0.176 Sum_probs=18.3
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
....+|+.+||||+...+..|..
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l~R 144 (154)
T TIGR02950 122 FSYKEIAELLNLSLAKVKSNLFR 144 (154)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHH
Confidence 45778899999999988877654
No 129
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=22.09 E-value=1.4e+02 Score=26.52 Aligned_cols=47 Identities=15% Similarity=0.280 Sum_probs=35.4
Q ss_pred cccceEEecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHH
Q psy7603 40 EEFVFEVLSTEEIVQHMIDCIKEVNNVVEIPATTTRILLNHFKWDKEKLM 89 (130)
Q Consensus 40 ~~~~y~vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLl 89 (130)
....+.-|+.++|...++..+++.. +.+++.... +|.+|.||.-.+.
T Consensus 256 ~~I~f~pL~~eei~~Il~~~a~k~~--i~is~~al~-~I~~y~~n~Rel~ 302 (531)
T TIGR02902 256 VEIFFRPLLDEEIKEIAKNAAEKIG--INLEKHALE-LIVKYASNGREAV 302 (531)
T ss_pred heeeCCCCCHHHHHHHHHHHHHHcC--CCcCHHHHH-HHHHhhhhHHHHH
Confidence 4566777889999999988888755 678888776 6677899864443
No 130
>COG2042 Uncharacterized conserved protein [Function unknown]
Probab=21.98 E-value=1.5e+02 Score=23.22 Aligned_cols=29 Identities=31% Similarity=0.672 Sum_probs=21.9
Q ss_pred hhhCCCHHHHHHHHHhCCCCh------HHHHHHHhc
Q psy7603 65 NVVEIPATTTRILLNHFKWDK------EKLMERYYD 94 (130)
Q Consensus 65 ~iL~vs~~~A~lLL~~fkWn~------ekLlE~y~e 94 (130)
-|+|. .+.|..||.+|+|-. .-++++|-.
T Consensus 126 YI~G~-~deA~~lls~F~WG~~FleLN~e~Le~Y~~ 160 (179)
T COG2042 126 YIVGF-KDEASELLSKFKWGHTFLELNKELLEEYSN 160 (179)
T ss_pred HHhCc-HHHHHHHHhhCcccHHHHHHhHHHHHHHHh
Confidence 45565 458999999999976 456777766
No 131
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=21.92 E-value=97 Score=23.05 Aligned_cols=24 Identities=13% Similarity=0.183 Sum_probs=19.4
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCC
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fk 82 (130)
...+|+.+|+||+..++..|..=+
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar 157 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRAR 157 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 357899999999999988877643
No 132
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=21.80 E-value=1.2e+02 Score=23.32 Aligned_cols=32 Identities=16% Similarity=0.254 Sum_probs=24.3
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
.+++|+.-++|++. .|.+||+ ||+.|++...+
T Consensus 26 smr~lA~~lgv~~~---slY~hf~-~K~~Ll~~~~~ 57 (205)
T PRK13756 26 TTRKLAQKLGVEQP---TLYWHVK-NKRALLDALAI 57 (205)
T ss_pred CHHHHHHHhCCCch---HHHHHcC-CHHHHHHHHHH
Confidence 46788899999875 4788997 88888655544
No 133
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=21.78 E-value=99 Score=22.16 Aligned_cols=22 Identities=32% Similarity=0.527 Sum_probs=17.7
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.+.+|+.+||||+..++..|..
T Consensus 137 s~~eiA~~lgis~~tv~~~l~R 158 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHR 158 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 5678899999999988877653
No 134
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=21.69 E-value=92 Score=22.73 Aligned_cols=23 Identities=13% Similarity=0.193 Sum_probs=18.3
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+++|+.+||||++.++..|..
T Consensus 154 ~s~~eIA~~lgis~~~v~~~l~R 176 (187)
T PRK12534 154 ITYEELAARTDTPIGTVKSWIRR 176 (187)
T ss_pred CCHHHHHHHhCCChhHHHHHHHH
Confidence 45678889999999888877764
No 135
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=21.55 E-value=98 Score=20.68 Aligned_cols=26 Identities=19% Similarity=0.213 Sum_probs=19.7
Q ss_pred EEecHHHHHHHHHHHHHHHhhhhCCC
Q psy7603 45 EVLSTEEIVQHMIDCIKEVNNVVEIP 70 (130)
Q Consensus 45 ~vLs~~eI~~~~~e~I~~V~~iL~vs 70 (130)
+.||.++|.+.++..+..+..-+++.
T Consensus 67 ~TLt~~ev~~~~~~i~~~l~~~~~~~ 92 (94)
T PF03147_consen 67 RTLTDEEVNEIHDKIIKALEKKLGAE 92 (94)
T ss_dssp S---HHHHHHHHHHHHHHHHHTCT-B
T ss_pred CCCCHHHHHHHHHHHHHHHHHHhCcE
Confidence 67999999999999999998888764
No 136
>TIGR01323 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations.
Probab=21.46 E-value=1.1e+02 Score=24.09 Aligned_cols=30 Identities=17% Similarity=0.245 Sum_probs=21.3
Q ss_pred CChHHHH-HHHhcCChhhHHHHcCCCCCCcce
Q psy7603 83 WDKEKLM-ERYYDGDQESSTLDYSASTSSGLV 113 (130)
Q Consensus 83 Wn~ekLl-E~y~e~D~~kvl~~aGl~~~~~~v 113 (130)
|=|..-. .+.-. ||.++|.+.|+..|....
T Consensus 107 WYks~~YRsRlVr-ePR~VL~EFGv~lP~~ve 137 (185)
T TIGR01323 107 WYKGFEYRARLVR-DPRGVLREFGTELPSDVE 137 (185)
T ss_pred ccCCHHHHHHHHH-CHHHHHHHhCCCCCCCeE
Confidence 5454333 33556 999999999999888554
No 137
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=21.29 E-value=1.1e+02 Score=22.17 Aligned_cols=22 Identities=14% Similarity=0.219 Sum_probs=17.1
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
...+|+++|++|++..+..|+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~r 158 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQ 158 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4577888889988888877754
No 138
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=21.25 E-value=1e+02 Score=22.03 Aligned_cols=23 Identities=17% Similarity=0.159 Sum_probs=18.8
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
....+|+.+|++|+..++..|+.
T Consensus 125 ~s~~eIA~~lgis~~tv~~~l~R 147 (165)
T PRK09644 125 LTYEEAASVLDLKLNTYKSHLFR 147 (165)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 34678999999999999887764
No 139
>PRK03636 hypothetical protein; Provisional
Probab=21.23 E-value=1.8e+02 Score=22.57 Aligned_cols=53 Identities=19% Similarity=0.222 Sum_probs=32.9
Q ss_pred HHHHHHHhCCCCh---HHHHHHHhcCChhhHHHHcCC-----CCCCcceeeeeecccCCcccccc
Q psy7603 73 TTRILLNHFKWDK---EKLMERYYDGDQESSTLDYSA-----STSSGLVFSAVDFGSGGSWFEFK 129 (130)
Q Consensus 73 ~A~lLL~~fkWn~---ekLlE~y~e~D~~kvl~~aGl-----~~~~~~v~~~~~~~~~~~~~~~~ 129 (130)
--+-+|.||.... -.++.-+.. -+.+|...+- ..|-++++|++| ++|..|-|.
T Consensus 11 Fi~wfL~~y~lK~Re~~wiLnyl~~--h~~lL~~VHFVe~~~~~~r~l~iS~~~--~~~~pF~F~ 71 (179)
T PRK03636 11 FLRWFLNNYQLKRRECVWILNYLMS--HDQLMEKVHFVENAEYCPRGLVMSAHG--VDDVPFRFF 71 (179)
T ss_pred HHHHHHHhccccchHHHHHHHHHHh--CHHHHhheeeeccccCCCceEEEEeec--cCCCceEEE
Confidence 3445666776655 233333333 3556666553 557799999998 577777764
No 140
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=21.20 E-value=1.1e+02 Score=18.55 Aligned_cols=24 Identities=21% Similarity=0.105 Sum_probs=18.1
Q ss_pred HHHHhhhhCCCHHHHHHHHHhCCC
Q psy7603 60 IKEVNNVVEIPATTTRILLNHFKW 83 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~fkW 83 (130)
+.+|+.+++|++...+.+.++-.+
T Consensus 3 ~~eva~~~gvs~~tlr~~~~~gli 26 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYERIGLL 26 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCC
Confidence 678999999999888866554333
No 141
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=21.09 E-value=84 Score=27.63 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=21.0
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhC
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~f 81 (130)
.|.+|+++|.+|+-.|++||++.
T Consensus 25 ~l~~la~~l~cs~R~~~~~l~~~ 47 (552)
T PRK13626 25 TLNELAELLNCSRRHMRTLLNTM 47 (552)
T ss_pred eHHHHHHHhcCChhHHHHHHHHH
Confidence 68899999999999999999874
No 142
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=21.09 E-value=50 Score=26.48 Aligned_cols=22 Identities=18% Similarity=0.226 Sum_probs=17.5
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
...+|+.+|+||++..+.+|..
T Consensus 244 s~~EIA~~Lgis~~tVk~~l~r 265 (285)
T TIGR02394 244 TLEEVAAEVGLTRERVRQIQVE 265 (285)
T ss_pred cHHHHHHHHCCCHHHHHHHHHH
Confidence 5788999999999888766543
No 143
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.98 E-value=1e+02 Score=22.85 Aligned_cols=24 Identities=8% Similarity=0.217 Sum_probs=21.0
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCC
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFK 82 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fk 82 (130)
-+.+|+.+|+|+.+....+++.|+
T Consensus 23 S~re~Ak~~gvs~sTvy~wv~r~~ 46 (138)
T COG3415 23 SCREAAKRFGVSISTVYRWVRRYR 46 (138)
T ss_pred cHHHHHHHhCccHHHHHHHHHHhc
Confidence 368899999999999999998876
No 144
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=20.91 E-value=1e+02 Score=23.09 Aligned_cols=21 Identities=19% Similarity=0.324 Sum_probs=17.2
Q ss_pred HHHHHhhhhCCCHHHHHHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~ 79 (130)
...+|+.+||+|++.++..|+
T Consensus 157 s~~EIA~~lgis~~tVk~~l~ 177 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLY 177 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567889999999988887765
No 145
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=20.87 E-value=1.3e+02 Score=17.02 Aligned_cols=21 Identities=14% Similarity=0.295 Sum_probs=15.2
Q ss_pred HHHHhhhhCCCHHHHHHHHHh
Q psy7603 60 IKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 60 I~~V~~iL~vs~~~A~lLL~~ 80 (130)
+.+|+..|++++..++-.|+.
T Consensus 13 ~~~i~~~l~is~~~v~~~l~~ 33 (66)
T smart00418 13 VCELAEILGLSQSTVSHHLKK 33 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 567777788888887766644
No 146
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.82 E-value=1.1e+02 Score=22.36 Aligned_cols=23 Identities=4% Similarity=0.221 Sum_probs=18.6
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+++|+.+|+||+...+..|..
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l~r 168 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGIHR 168 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 44678899999999998888754
No 147
>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=20.80 E-value=84 Score=22.82 Aligned_cols=22 Identities=5% Similarity=0.170 Sum_probs=13.0
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.+.+|+.+|+||+..++..|+.
T Consensus 118 s~~eIA~~lgis~~tV~~~l~R 139 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQR 139 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 3456666666666666555543
No 148
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=20.75 E-value=1.1e+02 Score=21.30 Aligned_cols=23 Identities=13% Similarity=0.179 Sum_probs=17.8
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+.+|+.+|++|+...+..|..
T Consensus 123 ~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 123 KTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 34678889999999888877653
No 149
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=20.59 E-value=1.8e+02 Score=21.48 Aligned_cols=32 Identities=16% Similarity=0.446 Sum_probs=24.5
Q ss_pred HHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 59 CIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
.|.+|+.-.||+++ .|.+||. +|+.|+...+.
T Consensus 33 t~~~Ia~~agvs~~---tlY~~F~-sKe~Ll~~v~~ 64 (215)
T PRK10668 33 SLADIAKAAGVTRG---AIYWHFK-NKSDLFSEIWE 64 (215)
T ss_pred CHHHHHHHhCCChH---HHHHHCC-CHHHHHHHHHH
Confidence 36777888888875 4889998 99888776654
No 150
>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=20.55 E-value=1.1e+02 Score=21.58 Aligned_cols=21 Identities=24% Similarity=0.241 Sum_probs=16.1
Q ss_pred HHHHHhhhhCCCHHHHHHHHH
Q psy7603 59 CIKEVNNVVEIPATTTRILLN 79 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~ 79 (130)
.+.+|+.+|+||+...+..|+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 357888888888888877664
No 151
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.48 E-value=1.1e+02 Score=22.56 Aligned_cols=22 Identities=18% Similarity=0.214 Sum_probs=17.6
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
...+|+.+|++|++.++..|+.
T Consensus 148 s~~EIA~~lgis~~tVk~~l~R 169 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVAR 169 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 3588999999999988877653
No 152
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=20.42 E-value=1.1e+02 Score=22.32 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=17.9
Q ss_pred HHHHHhhhhCCCHHHHHHHHHh
Q psy7603 59 CIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 59 ~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
.+.+|+.+|++|++..+..|..
T Consensus 140 s~~EIA~~lgis~~tVk~~l~R 161 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFER 161 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4578999999999998877654
No 153
>KOG3763|consensus
Probab=20.42 E-value=2.6e+02 Score=25.78 Aligned_cols=38 Identities=11% Similarity=0.294 Sum_probs=35.6
Q ss_pred HHHHHHHhhhhCCCHHHHHHHHHhCCCChHHHHHHHhc
Q psy7603 57 IDCIKEVNNVVEIPATTTRILLNHFKWDKEKLMERYYD 94 (130)
Q Consensus 57 ~e~I~~V~~iL~vs~~~A~lLL~~fkWn~ekLlE~y~e 94 (130)
.+.|.++....|+-+.-+.-+|..-+||-++.+..|.+
T Consensus 536 ~e~l~~~~~~tGln~~~s~~c~e~~nWdy~~A~k~F~~ 573 (585)
T KOG3763|consen 536 DEKLLKFQEETGLNSEWSTMCLEQNNWDYERALKLFIE 573 (585)
T ss_pred HHHHHHHHHHhcCChHHHHHHHHHccCCHHHHHHHHHH
Confidence 66788889999999999999999999999999999988
No 154
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=20.28 E-value=1.1e+02 Score=22.03 Aligned_cols=23 Identities=17% Similarity=0.502 Sum_probs=18.9
Q ss_pred HHHHHHhhhhCCCHHHHHHHHHh
Q psy7603 58 DCIKEVNNVVEIPATTTRILLNH 80 (130)
Q Consensus 58 e~I~~V~~iL~vs~~~A~lLL~~ 80 (130)
..+.+|+.+||+|+...+..|+.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~R 175 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHR 175 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 55788999999999998887753
No 155
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=20.26 E-value=2.2e+02 Score=19.05 Aligned_cols=33 Identities=9% Similarity=0.337 Sum_probs=23.0
Q ss_pred EecHHHHHHHHHHHHHHHhhhhCCCHHHHHHHHHhC
Q psy7603 46 VLSTEEIVQHMIDCIKEVNNVVEIPATTTRILLNHF 81 (130)
Q Consensus 46 vLs~~eI~~~~~e~I~~V~~iL~vs~~~A~lLL~~f 81 (130)
-+|.++........+. +.-++++..|+.+|..|
T Consensus 41 ~~t~eemie~~~~~~~---~~~~~~~~~a~~~~~~~ 73 (81)
T PF12674_consen 41 DITMEEMIEFCVPFMD---EFNGMTPEEARKMMPRY 73 (81)
T ss_pred cCCHHHHHHHHHHHHH---HhCCCCHHHHHHHHHHH
Confidence 4777776665555444 44449999999988765
Done!