Query psy648
Match_columns 72
No_of_seqs 74 out of 76
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 19:10:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy648.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/648hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10152 DUF2360: Predicted co 99.8 9E-20 1.9E-24 124.7 6.2 46 26-71 1-46 (148)
2 KOG4496|consensus 99.6 9E-15 2E-19 104.6 7.6 54 18-71 20-73 (194)
3 COG2960 Uncharacterized protei 94.4 0.86 1.9E-05 30.6 8.9 68 4-71 14-91 (103)
4 PF10393 Matrilin_ccoil: Trime 94.4 0.22 4.8E-06 29.0 5.4 33 37-69 14-46 (47)
5 PF04380 BMFP: Membrane fusoge 90.9 0.48 1E-05 29.5 3.8 47 23-69 26-73 (79)
6 PF10805 DUF2730: Protein of u 90.9 2.3 5E-05 27.5 7.2 57 12-71 4-60 (106)
7 TIGR01837 PHA_granule_1 poly(h 89.6 2.8 6E-05 27.7 6.8 37 31-67 81-117 (118)
8 PF05597 Phasin: Poly(hydroxya 89.4 3.1 6.8E-05 28.4 7.2 58 6-68 74-131 (132)
9 PF11471 Sugarporin_N: Maltopo 89.2 0.75 1.6E-05 27.7 3.6 30 41-70 27-56 (60)
10 PF10152 DUF2360: Predicted co 88.4 1.1 2.3E-05 30.7 4.3 39 22-64 8-46 (148)
11 PF04380 BMFP: Membrane fusoge 88.3 1.2 2.5E-05 27.7 4.1 29 39-68 51-79 (79)
12 TIGR02978 phageshock_pspC phag 84.9 1.8 3.9E-05 29.1 3.9 34 39-72 77-110 (121)
13 PRK10697 DNA-binding transcrip 84.7 1.9 4.1E-05 29.1 4.0 32 41-72 76-107 (118)
14 COG2960 Uncharacterized protei 80.0 5.1 0.00011 26.9 4.6 27 37-63 64-90 (103)
15 KOG4496|consensus 76.7 12 0.00025 27.4 5.9 39 31-69 22-64 (194)
16 TIGR02976 phageshock_pspB phag 75.5 7.3 0.00016 24.4 4.1 31 41-71 37-67 (75)
17 PF02090 SPAM: Salmonella surf 75.2 15 0.00032 26.1 6.0 32 39-70 16-47 (147)
18 cd04769 HTH_MerR2 Helix-Turn-H 74.3 11 0.00023 24.2 4.8 43 28-70 57-110 (116)
19 COG3937 Uncharacterized conser 70.6 11 0.00024 25.5 4.3 38 33-70 70-107 (108)
20 cd01282 HTH_MerR-like_sg3 Heli 70.6 18 0.0004 23.0 5.3 40 28-67 57-102 (112)
21 PF11471 Sugarporin_N: Maltopo 69.9 5.2 0.00011 24.0 2.4 23 48-70 27-49 (60)
22 PF06825 HSBP1: Heat shock fac 69.7 21 0.00045 21.2 5.5 29 38-66 17-48 (54)
23 PF10458 Val_tRNA-synt_C: Valy 69.3 12 0.00026 22.1 3.9 25 48-72 6-30 (66)
24 cd04770 HTH_HMRTR Helix-Turn-H 68.9 24 0.00052 22.5 5.5 38 29-66 59-99 (123)
25 cd01109 HTH_YyaN Helix-Turn-He 68.5 15 0.00032 23.3 4.5 39 29-67 59-100 (113)
26 PF09006 Surfac_D-trimer: Lung 67.9 12 0.00026 21.8 3.6 22 49-70 2-23 (46)
27 PF07195 FliD_C: Flagellar hoo 66.4 42 0.00091 23.9 6.9 30 41-70 195-224 (239)
28 PRK10227 DNA-binding transcrip 65.7 25 0.00054 23.4 5.3 25 45-69 85-109 (135)
29 PRK09458 pspB phage shock prot 64.5 18 0.00038 23.0 4.1 29 43-71 39-67 (75)
30 PLN02281 chlorophyllide a oxyg 64.0 30 0.00066 28.8 6.4 57 15-71 91-153 (536)
31 PF06667 PspB: Phage shock pro 63.9 18 0.0004 22.6 4.1 28 44-71 40-67 (75)
32 PRK09514 zntR zinc-responsive 63.9 24 0.00051 23.5 5.0 40 27-66 58-101 (140)
33 PF14965 BRI3BP: Negative regu 63.9 3.2 6.9E-05 30.1 0.7 36 34-70 141-176 (177)
34 PF04210 MtrG: Tetrahydrometha 62.9 13 0.00029 23.4 3.3 23 48-70 14-36 (70)
35 PF10241 KxDL: Uncharacterized 62.9 35 0.00076 21.3 7.9 53 18-71 30-82 (88)
36 PRK04406 hypothetical protein; 62.4 16 0.00034 22.6 3.6 19 50-68 8-26 (75)
37 cd04776 HTH_GnyR Helix-Turn-He 62.3 37 0.0008 22.0 5.5 40 28-67 56-101 (118)
38 cd01107 HTH_BmrR Helix-Turn-He 62.0 31 0.00068 21.8 5.0 32 39-70 75-106 (108)
39 TIGR02044 CueR Cu(I)-responsiv 61.7 20 0.00043 23.2 4.2 41 29-69 59-109 (127)
40 PF05480 Staph_haemo: Staphylo 61.4 29 0.00063 19.9 4.5 34 5-40 8-41 (43)
41 PF03105 SPX: SPX domain; Int 61.3 49 0.0011 22.5 6.6 43 18-67 92-134 (275)
42 PF04102 SlyX: SlyX; InterPro 61.2 15 0.00033 22.0 3.3 17 46-62 4-20 (69)
43 PRK15002 redox-sensitivie tran 61.1 30 0.00064 23.8 5.1 40 28-67 68-111 (154)
44 PF02996 Prefoldin: Prefoldin 60.0 40 0.00086 21.0 5.7 40 31-70 76-115 (120)
45 cd01109 HTH_YyaN Helix-Turn-He 59.6 22 0.00047 22.5 4.0 29 42-70 82-110 (113)
46 cd01282 HTH_MerR-like_sg3 Heli 59.5 22 0.00047 22.7 4.0 30 41-70 83-112 (112)
47 PF08702 Fib_alpha: Fibrinogen 59.2 32 0.00069 23.5 5.0 30 32-61 22-51 (146)
48 PRK09343 prefoldin subunit bet 59.2 21 0.00046 23.5 4.0 25 45-69 77-101 (121)
49 PF04508 Pox_A_type_inc: Viral 58.9 18 0.00038 18.3 2.8 17 48-64 3-19 (23)
50 PF08657 DASH_Spc34: DASH comp 58.6 20 0.00044 26.8 4.3 28 43-70 177-204 (259)
51 PRK13182 racA polar chromosome 58.1 18 0.00038 25.6 3.7 29 42-70 81-109 (175)
52 PRK02119 hypothetical protein; 58.0 17 0.00037 22.3 3.2 16 51-66 7-22 (73)
53 COG1382 GimC Prefoldin, chaper 58.0 20 0.00042 24.4 3.7 26 45-70 76-101 (119)
54 PF10779 XhlA: Haemolysin XhlA 57.6 26 0.00056 20.9 3.9 24 45-68 12-35 (71)
55 PF05278 PEARLI-4: Arabidopsis 57.4 43 0.00093 25.6 5.9 40 31-71 221-260 (269)
56 PF14193 DUF4315: Domain of un 57.1 26 0.00055 22.3 4.0 25 43-67 12-36 (83)
57 PF09278 MerR-DNA-bind: MerR, 56.9 34 0.00073 19.2 5.7 39 29-67 16-57 (65)
58 PRK02793 phi X174 lysis protei 56.7 16 0.00035 22.3 2.9 16 51-66 6-21 (72)
59 cd04787 HTH_HMRTR_unk Helix-Tu 56.3 54 0.0012 21.4 6.1 43 27-69 57-109 (133)
60 PF05531 NPV_P10: Nucleopolyhe 56.1 49 0.0011 20.9 5.8 23 48-70 37-59 (75)
61 cd00592 HTH_MerR-like Helix-Tu 55.6 28 0.00062 21.1 3.9 40 29-68 58-99 (100)
62 PF10046 BLOC1_2: Biogenesis o 55.5 51 0.0011 20.9 6.7 36 33-69 47-82 (99)
63 PF10779 XhlA: Haemolysin XhlA 55.1 26 0.00056 20.9 3.6 23 45-67 5-27 (71)
64 PRK08032 fliD flagellar cappin 55.0 77 0.0017 25.1 7.1 31 40-70 407-437 (462)
65 TIGR02051 MerR Hg(II)-responsi 54.7 37 0.0008 22.0 4.5 25 45-69 82-106 (124)
66 KOG3501|consensus 54.6 33 0.00072 23.4 4.4 46 22-70 53-98 (114)
67 PF15112 DUF4559: Domain of un 54.5 1E+02 0.0022 24.1 7.7 50 20-70 256-305 (307)
68 cd04785 HTH_CadR-PbrR-like Hel 53.8 58 0.0013 21.0 5.4 40 28-67 58-100 (126)
69 TIGR02047 CadR-PbrR Cd(II)/Pb( 53.4 53 0.0011 21.4 5.2 39 28-66 58-99 (127)
70 PF11853 DUF3373: Protein of u 53.4 35 0.00076 28.1 5.1 33 35-68 14-46 (489)
71 TIGR02043 ZntR Zn(II)-responsi 52.6 47 0.001 21.8 4.8 39 28-66 59-101 (131)
72 PF09340 NuA4: Histone acetylt 52.5 26 0.00057 21.8 3.4 14 51-64 14-27 (80)
73 PF14084 DUF4264: Protein of u 52.4 8.1 0.00018 23.0 1.0 10 30-39 16-25 (52)
74 PF11945 WASH_WAHD: WAHD domai 51.8 95 0.0021 23.8 7.0 20 45-64 49-68 (297)
75 KOG3684|consensus 51.8 62 0.0013 26.9 6.2 49 16-69 409-457 (489)
76 TIGR02132 phaR_Bmeg polyhydrox 51.5 96 0.0021 22.8 8.5 62 8-69 23-95 (189)
77 cd05511 Bromo_TFIID Bromodomai 51.0 36 0.00077 21.9 4.0 25 38-62 87-111 (112)
78 cd00632 Prefoldin_beta Prefold 51.0 33 0.00071 21.6 3.8 41 29-69 60-100 (105)
79 cd04783 HTH_MerR1 Helix-Turn-H 51.0 51 0.0011 21.2 4.8 40 30-69 60-107 (126)
80 PF11559 ADIP: Afadin- and alp 50.5 71 0.0015 21.1 9.4 63 8-70 42-104 (151)
81 PF07304 SRA1: Steroid recepto 49.9 35 0.00075 23.5 4.0 18 55-72 67-84 (157)
82 TIGR02894 DNA_bind_RsfA transc 49.8 69 0.0015 22.9 5.6 42 27-68 79-133 (161)
83 PF05377 FlaC_arch: Flagella a 49.7 25 0.00054 21.1 2.8 21 48-68 2-22 (55)
84 cd00632 Prefoldin_beta Prefold 49.1 65 0.0014 20.2 6.7 29 42-70 66-94 (105)
85 cd04775 HTH_Cfa-like Helix-Tur 49.1 42 0.00091 21.0 4.0 28 42-69 74-101 (102)
86 PF12699 phiKZ_IP: phiKZ-like 49.0 92 0.002 23.8 6.5 52 14-65 52-105 (339)
87 PF07047 OPA3: Optic atrophy 3 48.9 34 0.00074 22.8 3.8 27 44-70 103-129 (134)
88 PF02185 HR1: Hr1 repeat; Int 48.2 41 0.00089 19.7 3.7 30 40-69 34-63 (70)
89 cd01108 HTH_CueR Helix-Turn-He 48.2 74 0.0016 20.6 5.6 28 43-70 83-110 (127)
90 PF02996 Prefoldin: Prefoldin 47.8 50 0.0011 20.5 4.2 26 44-69 82-107 (120)
91 PF07195 FliD_C: Flagellar hoo 47.6 58 0.0013 23.2 5.0 63 6-70 138-217 (239)
92 PRK00736 hypothetical protein; 47.2 34 0.00073 20.6 3.2 19 46-64 5-23 (68)
93 PRK15471 chain length determin 46.9 1.3E+02 0.0028 23.0 7.7 38 20-59 149-186 (325)
94 PF06698 DUF1192: Protein of u 46.7 36 0.00079 20.5 3.3 23 48-70 23-45 (59)
95 PRK04325 hypothetical protein; 46.3 33 0.00072 21.0 3.1 21 45-65 8-28 (74)
96 PF13864 Enkurin: Calmodulin-b 46.3 34 0.00074 21.5 3.3 26 42-67 70-95 (98)
97 COG4064 MtrG Tetrahydromethano 46.2 37 0.0008 21.6 3.4 24 47-70 16-39 (75)
98 PF12718 Tropomyosin_1: Tropom 45.9 73 0.0016 21.6 5.1 27 43-69 32-58 (143)
99 cd04788 HTH_NolA-AlbR Helix-Tu 45.9 61 0.0013 20.0 4.4 37 27-66 57-93 (96)
100 PF15205 PLAC9: Placenta-speci 45.8 49 0.0011 21.0 3.9 23 46-71 25-47 (74)
101 PF06705 SF-assemblin: SF-asse 45.4 1.1E+02 0.0024 21.9 6.8 42 29-70 68-109 (247)
102 PF04740 LXG: LXG domain of WX 45.3 95 0.0021 21.0 6.7 50 21-70 68-123 (204)
103 PRK10636 putative ABC transpor 45.0 38 0.00083 27.6 4.1 26 46-71 563-588 (638)
104 cd04769 HTH_MerR2 Helix-Turn-H 44.5 81 0.0018 20.0 5.3 38 31-68 78-115 (116)
105 PF03670 UPF0184: Uncharacteri 43.8 45 0.00097 21.5 3.6 22 48-69 35-56 (83)
106 PRK14127 cell division protein 43.8 95 0.0021 20.6 5.6 25 46-70 44-68 (109)
107 PRK10227 DNA-binding transcrip 43.6 56 0.0012 21.8 4.2 41 29-69 59-102 (135)
108 cd04772 HTH_TioE_rpt1 First He 43.1 82 0.0018 19.6 5.4 39 30-68 59-98 (99)
109 PF13600 DUF4140: N-terminal d 43.0 59 0.0013 20.0 4.0 22 47-68 71-92 (104)
110 PF11690 DUF3287: Protein of u 42.7 31 0.00068 23.1 2.8 24 44-67 54-79 (109)
111 PF04533 Herpes_U44: Herpes vi 42.7 1E+02 0.0022 22.9 5.7 37 29-65 73-114 (210)
112 PF07716 bZIP_2: Basic region 42.3 63 0.0014 18.1 3.9 26 45-70 24-49 (54)
113 PRK10381 LPS O-antigen length 41.7 1.5E+02 0.0032 23.1 6.8 38 20-59 189-226 (377)
114 cd04784 HTH_CadR-PbrR Helix-Tu 41.7 94 0.002 19.9 5.5 40 27-66 57-99 (127)
115 PF13015 PRKCSH_1: Glucosidase 41.3 49 0.0011 22.9 3.7 27 45-71 2-28 (154)
116 PF05531 NPV_P10: Nucleopolyhe 41.2 57 0.0012 20.6 3.7 26 44-69 9-34 (75)
117 TIGR02051 MerR Hg(II)-responsi 40.9 63 0.0014 20.9 4.0 41 28-68 57-98 (124)
118 cd04789 HTH_Cfa Helix-Turn-Hel 40.9 66 0.0014 20.1 4.0 24 45-68 77-100 (102)
119 PF14257 DUF4349: Domain of un 40.7 54 0.0012 23.5 4.0 27 44-70 167-193 (262)
120 TIGR02044 CueR Cu(I)-responsiv 40.7 64 0.0014 20.8 4.0 31 34-64 81-111 (127)
121 PF02388 FemAB: FemAB family; 40.4 40 0.00088 26.0 3.5 22 46-67 273-294 (406)
122 cd04779 HTH_MerR-like_sg4 Heli 40.4 1.1E+02 0.0024 20.4 5.6 23 44-66 79-101 (134)
123 PF15361 RIC3: Resistance to i 40.2 33 0.00072 23.7 2.7 26 40-65 125-150 (152)
124 TIGR01950 SoxR redox-sensitive 40.2 1.1E+02 0.0023 20.6 5.1 42 29-70 59-111 (142)
125 PRK00295 hypothetical protein; 40.0 51 0.0011 19.8 3.2 13 47-59 6-18 (68)
126 KOG1853|consensus 39.8 74 0.0016 25.0 4.8 39 31-69 30-68 (333)
127 PRK08724 fliD flagellar cappin 39.8 1.2E+02 0.0026 26.1 6.4 62 7-70 574-648 (673)
128 cd04781 HTH_MerR-like_sg6 Heli 39.4 78 0.0017 20.2 4.2 28 43-70 78-105 (120)
129 cd04782 HTH_BltR Helix-Turn-He 39.4 93 0.002 19.2 4.8 38 28-67 58-95 (97)
130 PF11841 DUF3361: Domain of un 39.2 42 0.00092 23.7 3.2 35 26-71 56-90 (160)
131 PF00261 Tropomyosin: Tropomyo 38.8 1.4E+02 0.0031 21.3 5.9 27 43-69 187-213 (237)
132 PRK11638 lipopolysaccharide bi 38.8 1.8E+02 0.0039 22.4 7.6 38 20-59 170-207 (342)
133 COG5019 CDC3 Septin family pro 37.9 2.1E+02 0.0046 23.0 8.0 54 18-71 314-367 (373)
134 cd01108 HTH_CueR Helix-Turn-He 37.8 1.1E+02 0.0024 19.7 5.2 42 28-69 58-102 (127)
135 PF02388 FemAB: FemAB family; 37.5 1.9E+02 0.0042 22.3 8.2 27 43-69 239-265 (406)
136 PRK01026 tetrahydromethanopter 37.2 64 0.0014 20.6 3.5 22 48-69 17-38 (77)
137 PF04645 DUF603: Protein of un 36.8 1.1E+02 0.0024 22.4 5.0 36 35-70 94-129 (181)
138 cd01111 HTH_MerD Helix-Turn-He 36.8 1.1E+02 0.0024 19.4 5.5 44 27-70 57-104 (107)
139 cd04773 HTH_TioE_rpt2 Second H 36.8 1.1E+02 0.0024 19.3 5.5 42 28-69 58-101 (108)
140 PF04977 DivIC: Septum formati 36.6 84 0.0018 17.9 4.4 28 43-70 21-48 (80)
141 KOG1760|consensus 36.5 1.5E+02 0.0032 20.7 5.6 44 25-68 74-117 (131)
142 PF12152 eIF_4G1: Eukaryotic t 36.5 26 0.00057 22.0 1.6 15 34-48 58-72 (75)
143 cd04783 HTH_MerR1 Helix-Turn-H 36.3 82 0.0018 20.2 4.0 36 32-67 77-112 (126)
144 TIGR01149 mtrG N5-methyltetrah 35.5 72 0.0016 20.1 3.5 22 48-69 14-35 (70)
145 PF03520 KCNQ_channel: KCNQ vo 35.4 57 0.0012 24.2 3.4 25 42-66 152-176 (202)
146 PF04521 Viral_P18: ssRNA posi 35.3 60 0.0013 22.3 3.3 22 48-69 74-95 (120)
147 cd04776 HTH_GnyR Helix-Turn-He 35.0 1.3E+02 0.0027 19.4 6.3 34 36-69 84-117 (118)
148 PRK13723 conjugal transfer pil 34.8 2.2E+02 0.0049 23.2 7.0 48 20-71 390-437 (451)
149 PF13870 DUF4201: Domain of un 34.6 90 0.0019 21.2 4.2 38 32-70 139-176 (177)
150 PF14916 CCDC92: Coiled-coil d 34.5 42 0.0009 20.4 2.2 19 51-69 1-19 (60)
151 PF02609 Exonuc_VII_S: Exonucl 34.3 53 0.0012 18.5 2.6 17 42-58 37-53 (53)
152 PF01166 TSC22: TSC-22/dip/bun 34.2 1.1E+02 0.0024 18.6 4.3 28 43-70 18-45 (59)
153 TIGR01837 PHA_granule_1 poly(h 34.2 1.4E+02 0.0029 19.6 6.6 33 38-70 77-113 (118)
154 TIGR02047 CadR-PbrR Cd(II)/Pb( 34.1 92 0.002 20.2 4.0 28 43-70 83-110 (127)
155 PF04912 Dynamitin: Dynamitin 33.9 43 0.00093 25.7 2.7 21 44-64 207-227 (388)
156 PRK00846 hypothetical protein; 33.7 67 0.0015 20.2 3.1 16 51-66 11-26 (77)
157 cd00890 Prefoldin Prefoldin is 33.6 1.2E+02 0.0026 18.8 6.4 35 34-68 89-123 (129)
158 PF10066 DUF2304: Uncharacteri 33.5 71 0.0015 20.5 3.3 31 36-68 78-108 (115)
159 PRK09514 zntR zinc-responsive 33.1 1.5E+02 0.0032 19.7 5.2 32 38-69 80-111 (140)
160 PF14586 MHC_I_2: Class I Hist 33.1 61 0.0013 23.4 3.2 38 10-47 136-174 (174)
161 PF04420 CHD5: CHD5-like prote 32.9 78 0.0017 21.7 3.6 25 47-71 67-91 (161)
162 COG5187 RPN7 26S proteasome re 32.2 68 0.0015 25.9 3.6 39 30-68 77-118 (412)
163 PF15003 HAUS2: HAUS augmin-li 32.1 2.4E+02 0.0052 21.8 6.7 27 19-45 128-154 (277)
164 PF03954 Lectin_N: Hepatic lec 32.0 33 0.00071 24.0 1.7 33 37-69 71-103 (138)
165 PRK06798 fliD flagellar cappin 31.6 94 0.002 24.7 4.3 43 27-69 357-409 (440)
166 cd04777 HTH_MerR-like_sg1 Heli 31.4 1.3E+02 0.0029 18.6 5.5 42 28-69 56-104 (107)
167 PRK13182 racA polar chromosome 31.3 87 0.0019 22.1 3.7 26 44-69 90-115 (175)
168 cd03182 GST_C_GTT2_like GST_C 31.3 99 0.0022 18.3 3.6 22 50-71 46-67 (117)
169 PF13220 DUF4028: Protein of u 31.0 33 0.00071 21.1 1.3 12 10-21 44-56 (65)
170 PF14435 SUKH-4: SUKH-4 immuni 30.9 87 0.0019 20.8 3.6 46 23-69 109-157 (179)
171 PF07439 DUF1515: Protein of u 30.9 1.2E+02 0.0026 20.6 4.2 29 43-71 37-65 (112)
172 TIGR02231 conserved hypothetic 30.6 2.3E+02 0.005 22.4 6.4 25 45-69 144-168 (525)
173 cd03184 GST_C_Omega GST_C fami 30.6 1.3E+02 0.0029 18.4 5.6 46 17-70 4-49 (124)
174 PF13805 Pil1: Eisosome compon 30.5 67 0.0015 24.6 3.2 26 45-70 164-189 (271)
175 COG5509 Uncharacterized small 30.3 90 0.002 19.4 3.2 24 48-71 27-50 (65)
176 TIGR01280 xseB exodeoxyribonuc 30.2 67 0.0015 19.3 2.6 19 41-59 38-56 (67)
177 PF02370 M: M protein repeat; 30.0 80 0.0017 15.6 2.9 16 51-66 6-21 (21)
178 TIGR02338 gimC_beta prefoldin, 29.8 1.5E+02 0.0033 18.8 6.1 27 43-69 78-104 (110)
179 PF08393 DHC_N2: Dynein heavy 29.7 79 0.0017 23.6 3.5 27 42-68 280-307 (408)
180 cd01106 HTH_TipAL-Mta Helix-Tu 29.6 1.4E+02 0.0031 18.4 4.7 38 29-66 59-100 (103)
181 PF12125 Beta-TrCP_D: D domain 29.5 44 0.00095 19.0 1.6 22 15-36 5-26 (40)
182 smart00741 SapB Saposin (B) Do 29.2 1E+02 0.0022 16.7 7.0 45 8-52 8-53 (76)
183 PF10400 Vir_act_alpha_C: Viru 28.9 1.3E+02 0.0028 17.6 4.5 27 31-57 20-46 (90)
184 PRK11147 ABC transporter ATPas 28.8 93 0.002 25.2 3.9 24 48-71 570-593 (635)
185 KOG1029|consensus 28.3 3.1E+02 0.0066 25.0 7.1 64 6-70 402-468 (1118)
186 PF11853 DUF3373: Protein of u 28.2 58 0.0013 26.9 2.7 27 45-71 30-56 (489)
187 PHA03385 IX capsid protein IX, 28.1 1.5E+02 0.0032 20.8 4.3 29 42-70 96-124 (135)
188 PRK13752 putative transcriptio 28.0 1.9E+02 0.0042 19.4 6.3 39 29-67 66-112 (144)
189 PRK00965 tetrahydromethanopter 28.0 76 0.0016 20.9 2.8 23 48-70 33-55 (96)
190 PF08826 DMPK_coil: DMPK coile 27.7 1.4E+02 0.0031 17.9 4.6 27 43-69 29-55 (61)
191 PF12709 Kinetocho_Slk19: Cent 27.7 1.8E+02 0.0038 18.9 4.7 50 22-71 25-74 (87)
192 PRK14063 exodeoxyribonuclease 27.5 77 0.0017 19.5 2.6 17 42-58 43-59 (76)
193 KOG4603|consensus 27.5 1.3E+02 0.0029 22.3 4.2 28 43-70 83-110 (201)
194 PF13410 GST_C_2: Glutathione 27.4 1.1E+02 0.0025 16.6 3.7 21 51-71 4-24 (69)
195 PF06013 WXG100: Proteins of 1 27.3 1.2E+02 0.0026 16.7 4.6 30 37-66 9-38 (86)
196 PF13314 DUF4083: Domain of un 27.2 1.1E+02 0.0023 18.6 3.1 15 50-67 43-57 (58)
197 PF12841 YvrJ: YvrJ protein fa 27.0 1.2E+02 0.0026 16.7 3.1 18 48-65 17-34 (38)
198 PF03285 Paralemmin: Paralemmi 26.5 90 0.0019 24.0 3.3 24 45-68 9-32 (278)
199 cd04790 HTH_Cfa-like_unk Helix 26.4 2.2E+02 0.0048 19.5 6.0 41 30-70 61-105 (172)
200 COG1590 Uncharacterized conser 26.3 2.3E+02 0.005 21.1 5.3 36 35-70 161-196 (208)
201 PRK06664 fliD flagellar hook-a 26.3 2.5E+02 0.0054 23.8 6.1 43 27-69 578-630 (661)
202 smart00189 IL2 Interleukin-2 f 26.3 65 0.0014 22.9 2.4 34 18-51 102-153 (154)
203 PF12507 HCMV_UL139: Human Cyt 26.1 1.1E+02 0.0024 21.1 3.3 28 43-70 34-61 (121)
204 COG5521 Predicted integral mem 26.0 1.6E+02 0.0036 22.8 4.6 38 5-42 155-194 (275)
205 PRK11239 hypothetical protein; 25.9 1.4E+02 0.003 22.4 4.1 21 49-69 186-206 (215)
206 smart00338 BRLZ basic region l 25.8 1.4E+02 0.003 17.0 4.0 22 48-69 28-49 (65)
207 COG4476 Uncharacterized protei 25.8 48 0.001 21.8 1.5 30 14-51 8-37 (90)
208 PF10975 DUF2802: Protein of u 25.8 1.2E+02 0.0026 18.4 3.2 23 45-67 4-26 (70)
209 KOG1419|consensus 25.7 90 0.0019 26.8 3.4 23 43-65 566-588 (654)
210 TIGR01834 PHA_synth_III_E poly 25.4 3.3E+02 0.0072 21.3 8.3 53 18-70 250-313 (320)
211 TIGR01834 PHA_synth_III_E poly 25.4 91 0.002 24.4 3.2 26 44-69 294-319 (320)
212 PRK14064 exodeoxyribonuclease 25.4 83 0.0018 19.4 2.5 18 41-58 43-60 (75)
213 PRK05892 nucleoside diphosphat 25.3 80 0.0017 21.7 2.6 19 53-71 54-72 (158)
214 PF15397 DUF4618: Domain of un 25.2 74 0.0016 24.1 2.6 17 54-70 82-98 (258)
215 cd04770 HTH_HMRTR Helix-Turn-H 25.1 1.9E+02 0.004 18.3 6.1 29 41-69 81-109 (123)
216 PRK13710 plasmid maintenance p 25.1 1.4E+02 0.003 18.4 3.4 34 6-39 33-68 (72)
217 PF12958 DUF3847: Protein of u 25.0 1.9E+02 0.0042 18.5 5.0 30 37-66 6-35 (86)
218 PRK00977 exodeoxyribonuclease 24.7 93 0.002 19.3 2.6 18 41-58 47-64 (80)
219 PF10552 ORF6C: ORF6C domain; 24.7 1.3E+02 0.0029 19.3 3.5 20 47-66 9-28 (116)
220 PRK04387 hypothetical protein; 24.6 49 0.0011 21.6 1.4 17 13-29 7-23 (90)
221 PF00517 GP41: Retroviral enve 24.2 2.7E+02 0.0058 19.8 8.4 51 19-69 12-62 (204)
222 PF14805 THDPS_N_2: Tetrahydro 24.2 1E+02 0.0022 18.9 2.7 18 7-24 1-18 (70)
223 PF05549 Allexi_40kDa: Allexiv 24.1 1.5E+02 0.0032 23.0 4.1 21 21-41 52-72 (271)
224 COG0732 HsdS Restriction endon 23.7 2.7E+02 0.0058 19.6 5.4 39 30-69 349-387 (391)
225 PRK14981 DNA-directed RNA poly 23.6 2.1E+02 0.0046 18.5 4.3 46 10-59 18-63 (112)
226 cd04768 HTH_BmrR-like Helix-Tu 23.6 1.9E+02 0.0041 17.8 4.6 36 29-67 59-94 (96)
227 PF07426 Dynactin_p22: Dynacti 23.5 82 0.0018 22.2 2.5 15 48-62 7-21 (174)
228 PF12329 TMF_DNA_bd: TATA elem 23.5 1.8E+02 0.004 17.6 4.1 34 37-70 38-71 (74)
229 PF00261 Tropomyosin: Tropomyo 23.4 2.8E+02 0.0061 19.8 7.4 27 43-69 173-199 (237)
230 PF01420 Methylase_S: Type I r 23.4 1.8E+02 0.0039 17.8 3.8 11 32-42 143-153 (167)
231 PF14712 Snapin_Pallidin: Snap 23.4 1.8E+02 0.0039 17.5 6.3 21 43-63 68-88 (92)
232 PRK11239 hypothetical protein; 23.1 1.3E+02 0.0028 22.5 3.5 27 44-70 188-214 (215)
233 PRK14070 exodeoxyribonuclease 22.9 1E+02 0.0022 18.9 2.5 19 41-59 32-50 (69)
234 PF09823 DUF2357: Domain of un 22.9 2.6E+02 0.0057 19.2 5.9 17 25-41 168-184 (248)
235 PRK13729 conjugal transfer pil 22.8 2E+02 0.0044 23.8 4.9 24 46-69 97-120 (475)
236 PF02403 Seryl_tRNA_N: Seryl-t 22.6 2E+02 0.0043 17.7 4.2 24 47-70 75-98 (108)
237 PRK14067 exodeoxyribonuclease 22.5 1E+02 0.0022 19.3 2.5 18 42-59 45-62 (80)
238 PRK00888 ftsB cell division pr 22.4 2E+02 0.0044 18.5 4.0 23 46-68 34-56 (105)
239 PF14063 DUF4254: Protein of u 22.4 2.3E+02 0.005 19.5 4.5 29 43-71 110-138 (145)
240 PF04568 IATP: Mitochondrial A 22.4 2.4E+02 0.0051 18.5 4.9 27 43-69 69-99 (100)
241 PRK12765 flagellar capping pro 22.3 1.6E+02 0.0034 24.5 4.2 34 37-70 530-563 (595)
242 PF09177 Syntaxin-6_N: Syntaxi 22.3 1.6E+02 0.0035 18.2 3.4 25 43-67 43-67 (97)
243 PF00715 IL2: Interleukin 2 Th 22.3 1.1E+02 0.0023 21.7 2.8 30 18-47 96-143 (145)
244 PF11435 She2p: RNA binding pr 22.3 1.3E+02 0.0027 22.5 3.3 25 21-45 5-29 (204)
245 PF04297 UPF0122: Putative hel 22.0 2.4E+02 0.0052 18.4 5.5 53 5-61 22-74 (101)
246 PF11944 DUF3461: Protein of u 21.6 1.6E+02 0.0035 20.3 3.5 25 33-57 100-124 (125)
247 PF12761 End3: Actin cytoskele 21.5 1.3E+02 0.0029 22.0 3.2 25 47-71 161-185 (195)
248 PF08537 NBP1: Fungal Nap bind 21.5 1.7E+02 0.0037 23.1 4.0 24 46-69 182-205 (323)
249 KOG4090|consensus 21.4 2.2E+02 0.0047 20.4 4.2 33 15-47 118-152 (157)
250 cd03202 GST_C_etherase_LigE GS 21.4 1.1E+02 0.0024 19.3 2.6 32 40-71 45-76 (124)
251 PF09597 IGR: IGR protein moti 21.3 1.5E+02 0.0033 17.6 3.0 22 35-56 3-24 (57)
252 PF10444 Nbl1_Borealin_N: Nbl1 21.2 1.8E+02 0.0039 16.7 4.7 23 34-56 4-26 (59)
253 PF05557 MAD: Mitotic checkpoi 21.1 1.6E+02 0.0034 24.5 4.0 28 44-71 508-535 (722)
254 PF10211 Ax_dynein_light: Axon 21.0 3.1E+02 0.0067 19.3 8.2 24 46-69 120-143 (189)
255 PRK14069 exodeoxyribonuclease 20.8 1.1E+02 0.0024 20.0 2.5 18 42-59 46-63 (95)
256 cd04766 HTH_HspR Helix-Turn-He 20.6 2.1E+02 0.0045 17.2 3.8 24 47-70 66-89 (91)
257 cd04786 HTH_MerR-like_sg7 Heli 20.6 2.6E+02 0.0057 18.4 5.9 26 44-69 83-108 (131)
258 PF10112 Halogen_Hydrol: 5-bro 20.6 3E+02 0.0064 18.9 5.2 49 21-69 126-176 (199)
259 PF08946 Osmo_CC: Osmosensory 20.3 2E+02 0.0043 16.8 4.3 32 37-68 10-41 (46)
260 PF15397 DUF4618: Domain of un 20.3 3.1E+02 0.0068 20.8 5.1 60 9-68 40-103 (258)
261 PF02994 Transposase_22: L1 tr 20.2 1.8E+02 0.0039 22.5 3.9 21 46-66 144-164 (370)
262 TIGR02169 SMC_prok_A chromosom 20.2 4.6E+02 0.0099 22.0 6.4 38 32-70 164-201 (1164)
263 PF13974 YebO: YebO-like prote 20.2 2.5E+02 0.0054 17.9 4.7 31 35-65 16-46 (80)
264 PRK01885 greB transcription el 20.1 1.2E+02 0.0027 20.7 2.8 17 54-70 55-71 (157)
265 PF05256 UPF0223: Uncharacteri 20.0 85 0.0018 20.3 1.8 18 12-29 6-23 (88)
266 PF15188 CCDC-167: Coiled-coil 20.0 1.9E+02 0.004 18.6 3.4 13 43-55 16-28 (85)
No 1
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=99.80 E-value=9e-20 Score=124.71 Aligned_cols=46 Identities=30% Similarity=0.528 Sum_probs=45.3
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 26 ITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 26 in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
|||||.||++|||+|+.+||+||..++.|||++|++|.||||||+|
T Consensus 1 vN~Fi~~tv~fLN~F~~~cE~kL~~~e~~Lq~~E~~l~iLEaKL~S 46 (148)
T PF10152_consen 1 VNHFIVHTVQFLNRFASVCEEKLSDMEQRLQRLEATLNILEAKLSS 46 (148)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 6999999999999999999999999999999999999999999988
No 2
>KOG4496|consensus
Probab=99.57 E-value=9e-15 Score=104.62 Aligned_cols=54 Identities=22% Similarity=0.407 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 18 ANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 18 ~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
++.+.++|+|+||+|+++|||+|.+.|+.+|+.++.+|++.||+|++|||||++
T Consensus 20 dh~RTaaf~N~fimh~tefLN~F~n~cEd~Lad~elridq~d~kLnildaKLa~ 73 (194)
T KOG4496|consen 20 DHHRTAAFFNCFIMHMTEFLNNFGNKCEDILADAELRIDQADRKLNILDAKLAG 73 (194)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 356788999999999999999999999999999999999999999999999986
No 3
>COG2960 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.36 E-value=0.86 Score=30.58 Aligned_cols=68 Identities=34% Similarity=0.374 Sum_probs=50.3
Q ss_pred HhHHHHHHHHHhhhHH--HHHHHHHHHhHHHHH-HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 4 VHREAIQKQIQQDWAN--REYIEIITGSIKKIT-DFLNSFDMSCRSR-------LAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 4 ~~~~~v~~~iq~DW~n--Re~i~~in~~I~~~~-~FLN~F~~sc~~k-------La~ln~KL~~LE~~L~~LEAklss 71 (72)
-+.+++..++..|-.+ +++-+-|-..|+-+. .-||+.|.+.|+- |..--+||..||.++.-|||++++
T Consensus 14 ~~~e~~~~ql~e~~a~~~~~~~~evE~~~r~~~q~~lnkLDlVsREEFdvq~qvl~rtR~kl~~Leari~~LEarl~~ 91 (103)
T COG2960 14 NRFEDIAAQLSEDAAGAAQEVRAEVEKAFRAQLQRQLNKLDLVSREEFDVQRQVLLRTREKLAALEARIEELEARLAS 91 (103)
T ss_pred HHHHHHHHHHHHHccccchhhHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3567788888888877 566666666666554 4688888877765 445567899999999999999863
No 4
>PF10393 Matrilin_ccoil: Trimeric coiled-coil oligomerisation domain of matrilin; InterPro: IPR019466 This entry represents a short domain found the matrilin (cartilage matrix) proteins. It forms a coiled coil structure and contains a single cysteine residue at its start which is likely to form a di-sulphide bridge with a corresponding cysteine in an upstream EGF domain (IPR006209 from INTERPRO), thereby spanning the VWA domain of the protein (IPR002035 from INTERPRO).This domain is likely to be responsible for protein trimerisation []. ; PDB: 1AQ5_C.
Probab=94.36 E-value=0.22 Score=28.97 Aligned_cols=33 Identities=36% Similarity=0.510 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 37 LNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 37 LN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
+-.|-....+.|.+|+.||..+.++|+-||.++
T Consensus 14 lv~FQ~~v~~~lq~Lt~kL~~vs~RLe~LEn~~ 46 (47)
T PF10393_consen 14 LVAFQNKVTSALQSLTQKLDAVSKRLEALENRL 46 (47)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 345777888899999999999999999999876
No 5
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=90.90 E-value=0.48 Score=29.45 Aligned_cols=47 Identities=26% Similarity=0.323 Sum_probs=27.6
Q ss_pred HHHHHHhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 23 IEIITGSIKKI-TDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 23 i~~in~~I~~~-~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..-+-.+|+.. -.+|++++.+.|+=+.....-|.++..+|+-||++|
T Consensus 26 ~~e~e~~~r~~l~~~l~kldlVtREEFd~q~~~L~~~r~kl~~LEarl 73 (79)
T PF04380_consen 26 REEIEKNIRARLQSALSKLDLVTREEFDAQKAVLARTREKLEALEARL 73 (79)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344445443 357888888888877666555555444444444444
No 6
>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins. The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.
Probab=90.90 E-value=2.3 Score=27.52 Aligned_cols=57 Identities=21% Similarity=0.326 Sum_probs=38.9
Q ss_pred HHHhhhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 12 QIQQDWANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 12 ~iq~DW~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
.|+++|.= +.+.+...+.-+.-.|.+ .-.-++.+..+.++++..+++|..+|.++..
T Consensus 4 ~~~~~w~i--i~a~~~~~~~~~~~~l~~-~~a~~~~~~~l~~~~~~~~~Rl~~lE~~l~~ 60 (106)
T PF10805_consen 4 FIKKNWGI--IWAVFGIAGGIFWLWLRR-TYAKREDIEKLEERLDEHDRRLQALETKLEH 60 (106)
T ss_pred HHHhCcHH--HHHHHHHHHHHHHHHHHH-hhccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46777765 455554444444444444 3345889999989999999999999988754
No 7
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=89.55 E-value=2.8 Score=27.70 Aligned_cols=37 Identities=22% Similarity=0.457 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 31 KKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 31 ~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
..+-++|+++....++-+..|+.||..||++|.-|+.
T Consensus 81 ~~v~~~L~~lg~~tk~ev~~L~~RI~~Le~~l~~l~~ 117 (118)
T TIGR01837 81 ERVEQALNRLNIPSREEIEALSAKIEQLAVQVEELRR 117 (118)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4556889999999999999999999999999988763
No 8
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=89.42 E-value=3.1 Score=28.36 Aligned_cols=58 Identities=16% Similarity=0.383 Sum_probs=47.0
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 6 REAIQKQIQQDWANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 6 ~~~v~~~iq~DW~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
.+++...+..-|++=| +.|=.+....||++..-.+.=+..|+.||..|++.|+-|..+
T Consensus 74 ~~~~~~~~~~~~dklE-----~~fd~rV~~aL~rLgvPs~~dv~~L~~rId~L~~~v~~l~~~ 131 (132)
T PF05597_consen 74 VDDVKERATGQWDKLE-----QAFDERVARALNRLGVPSRKDVEALSARIDQLTAQVERLANK 131 (132)
T ss_pred HHHHHHHHHHHHHHHH-----HHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4567777888887533 345566788999999999999999999999999999988653
No 9
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=89.18 E-value=0.75 Score=27.67 Aligned_cols=30 Identities=33% Similarity=0.498 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 41 DMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..+-|.||+.|+.+|+..|.++.--|+++.
T Consensus 27 ~ltiEqRLa~LE~rL~~ae~ra~~ae~~~~ 56 (60)
T PF11471_consen 27 PLTIEQRLAALEQRLQAAEQRAQAAEARAK 56 (60)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345689999999999999999988888765
No 10
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=88.43 E-value=1.1 Score=30.72 Aligned_cols=39 Identities=18% Similarity=0.284 Sum_probs=28.1
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 22 YIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEY 64 (72)
Q Consensus 22 ~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~ 64 (72)
.+.|+|.|-...=+=|.++ +.||..++-+|..||++|.=
T Consensus 8 tv~fLN~F~~~cE~kL~~~----e~~Lq~~E~~l~iLEaKL~S 46 (148)
T PF10152_consen 8 TVQFLNRFASVCEEKLSDM----EQRLQRLEATLNILEAKLSS 46 (148)
T ss_pred HHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHhc
Confidence 4677888877666656544 46788888888888888753
No 11
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=88.26 E-value=1.2 Score=27.68 Aligned_cols=29 Identities=45% Similarity=0.586 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 39 SFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 39 ~F~~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
.|+ .-..-|+.+.+||..||++|.-||++
T Consensus 51 EFd-~q~~~L~~~r~kl~~LEarl~~LE~~ 79 (79)
T PF04380_consen 51 EFD-AQKAVLARTREKLEALEARLAALEAQ 79 (79)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 566 45677888889999999999999875
No 12
>TIGR02978 phageshock_pspC phage shock protein C. All members of this protein family are the phage shock protein PspC. These proteins contain a PspC domain, as do other members of the larger family of proteins described by Pfam model pfam04024. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor, PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin overexpression, ethanol, heat shock, and protein export defects.
Probab=84.89 E-value=1.8 Score=29.15 Aligned_cols=34 Identities=24% Similarity=0.299 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy648 39 SFDMSCRSRLAVLNEKLTTLERRIEYLEARKSHG 72 (72)
Q Consensus 39 ~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss~ 72 (72)
+-..+-+.-|.++++++..+|++|.-+|+-|+|.
T Consensus 77 ~~~~~~~~~l~~~~~~~~~~e~Rl~~mE~yVTS~ 110 (121)
T TIGR02978 77 QAGQSPRQALREVKREFRDLERRLRNMERYVTSD 110 (121)
T ss_pred hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4456788899999999999999999999999883
No 13
>PRK10697 DNA-binding transcriptional activator PspC; Provisional
Probab=84.71 E-value=1.9 Score=29.12 Aligned_cols=32 Identities=19% Similarity=0.218 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Q psy648 41 DMSCRSRLAVLNEKLTTLERRIEYLEARKSHG 72 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~LE~~L~~LEAklss~ 72 (72)
..+-+.-|.++++++..+|++|.-+|.-|+|.
T Consensus 76 ~~s~~~~l~~~~~~~~~~e~Rlr~mE~yVTS~ 107 (118)
T PRK10697 76 QPSSSELLDEVDRELAAGEQRLREMERYVTSD 107 (118)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 34678889999999999999999999999883
No 14
>COG2960 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.96 E-value=5.1 Score=26.88 Aligned_cols=27 Identities=26% Similarity=0.444 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 37 LNSFDMSCRSRLAVLNEKLTTLERRIE 63 (72)
Q Consensus 37 LN~F~~sc~~kLa~ln~KL~~LE~~L~ 63 (72)
.-.--..+|+||+.|+.|+..||.++.
T Consensus 64 q~qvl~rtR~kl~~Leari~~LEarl~ 90 (103)
T COG2960 64 QRQVLLRTREKLAALEARIEELEARLA 90 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344456799999999999999999986
No 15
>KOG4496|consensus
Probab=76.73 E-value=12 Score=27.37 Aligned_cols=39 Identities=23% Similarity=0.314 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhh
Q psy648 31 KKITDFLNSFDMSCRSRLAV----LNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 31 ~~~~~FLN~F~~sc~~kLa~----ln~KL~~LE~~L~~LEAkl 69 (72)
.+|+-|+|+|-..+-+-|.. .+++|..+|.+|+..|-+|
T Consensus 22 ~RTaaf~N~fimh~tefLN~F~n~cEd~Lad~elridq~d~kL 64 (194)
T KOG4496|consen 22 HRTAAFFNCFIMHMTEFLNNFGNKCEDILADAELRIDQADRKL 64 (194)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 35677777777776666654 3556666666666666554
No 16
>TIGR02976 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response.
Probab=75.55 E-value=7.3 Score=24.38 Aligned_cols=31 Identities=29% Similarity=0.255 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 41 DMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
+..=+.+|..|.++.+++|.+++.||.=|..
T Consensus 37 s~~d~~~L~~L~~~a~rm~eRI~tLE~ILd~ 67 (75)
T TIGR02976 37 STDDQALLQELYAKADRLEERIDTLERILDA 67 (75)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 3445678999999999999999999987654
No 17
>PF02090 SPAM: Salmonella surface presentation of antigen gene type M protein; InterPro: IPR002954 The Salmonella typhimurium Surface Presentation of Antigens M gene (SpaM) is one of 12 that form a cluster responsible for invasion properties []. The gene product is required for entry by the bacterium into epithelial cells, and is thus considered to be a virulence factor []. Other Spa genes in the cluster are related to invasion (Inv) genes in similar Salmonella and Shigella species [], and flagella biosynthesis genes in Helicobacter pylori []. A homologue of this protein has been found recently in Salmonella enterica []. The protein, named InvI, is required by the organism to gain access to mammalian epithelial cells, and cellular mutants (InvI-) failed to successfully infect these cells. It has also been found that the inv-spa loci of this particular species encode for a type III protein secretion system, essential in the bacterium's host cell invasion process [].
Probab=75.22 E-value=15 Score=26.09 Aligned_cols=32 Identities=22% Similarity=0.399 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 39 SFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 39 ~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
-|-+.|+..|..++.+.+.|+++..-+|++++
T Consensus 16 ~~~~rCe~~L~ql~~e~~~L~~ee~~~~~Q~~ 47 (147)
T PF02090_consen 16 MFQSRCEQALLQLQREEQKLDAEEEAIEEQRA 47 (147)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 36778999999999999999999999998864
No 18
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=74.28 E-value=11 Score=24.19 Aligned_cols=43 Identities=9% Similarity=0.236 Sum_probs=25.4
Q ss_pred HhHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 28 GSIKKITDFLNSFD-----------MSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 28 ~~I~~~~~FLN~F~-----------~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..|..|-++++..+ ...+.++..+++++..+++.+..|+..+.
T Consensus 57 ~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~ 110 (116)
T cd04769 57 FTLAELKAIFAGHEGRAVLPWPHLQQALEDKKQEIRAQITELQQLLARLDAFEA 110 (116)
T ss_pred CCHHHHHHHHhccccCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556666665543 23555666666666666666666666554
No 19
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=70.64 E-value=11 Score=25.45 Aligned_cols=38 Identities=26% Similarity=0.517 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 33 ITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 33 ~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
|-+-+...+...++-...++++++.||+++.-||+++.
T Consensus 70 i~~ml~~~~~~r~~~~~~l~~rvd~Lerqv~~Lenk~k 107 (108)
T COG3937 70 IEEMLSDLEVARQSEMDELTERVDALERQVADLENKLK 107 (108)
T ss_pred HHHHHhhccccccchHHHHHHHHHHHHHHHHHHHHHhc
Confidence 33344455566677788999999999999999999863
No 20
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=70.62 E-value=18 Score=23.03 Aligned_cols=40 Identities=30% Similarity=0.539 Sum_probs=21.8
Q ss_pred HhHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 28 GSIKKITDFLNSFD------MSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 28 ~~I~~~~~FLN~F~------~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
..+..|-++++.+. .+|......++.+++.++.++.-|+.
T Consensus 57 ~sl~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (112)
T cd01282 57 LTLEEIREFLPCLRGGEPTFRPCPDLLAVLRRELARIDRQIADLTR 102 (112)
T ss_pred CCHHHHHHHHHHhhCCCccCCccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666777777653 34555555555555555555544443
No 21
>PF11471 Sugarporin_N: Maltoporin periplasmic N-terminal extension; InterPro: IPR021570 This N-terminal domain is found in members of the sugar porin family 1.B.3 from TC, They are related to LamB - the well characterised maltoporin of Escherichia coli for which the three-dimensional structures with and without its substrate have been obtained by X-ray diffraction. The protein consists of an 18 beta-stranded beta-barrel in contrast to proteins of the general bacterial porin family (GBP) and the Rhodobacter PorCa Porin (RPP) family which consist of 16 beta-stranded beta-barrels. Although maltoporin contains a wider beta-barrel than the porins of the GBP and RPP families (1.B.1 from TC and 1.B.7 from TC), it exhibits a narrower channel, showing only 5% of the ionic conductance of the latter porins.
Probab=69.86 E-value=5.2 Score=23.98 Aligned_cols=23 Identities=26% Similarity=0.473 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Q psy648 48 LAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkls 70 (72)
-.++++||..||.+|.-.|.+..
T Consensus 27 ~ltiEqRLa~LE~rL~~ae~ra~ 49 (60)
T PF11471_consen 27 PLTIEQRLAALEQRLQAAEQRAQ 49 (60)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHH
Confidence 34689999999999988887764
No 22
>PF06825 HSBP1: Heat shock factor binding protein 1; InterPro: IPR009643 Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response [].; PDB: 3CI9_A.
Probab=69.73 E-value=21 Score=21.19 Aligned_cols=29 Identities=21% Similarity=0.402 Sum_probs=17.5
Q ss_pred HHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 38 NSFDM---SCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 38 N~F~~---sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
++|.. ..-.|+..+..||+.||+++.-|=
T Consensus 17 ~kFq~mS~~I~~riDeM~~RIDdLE~si~dl~ 48 (54)
T PF06825_consen 17 DKFQTMSDQILGRIDEMSSRIDDLEKSIADLM 48 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCCHHHH----
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 44544 445677777888888888876553
No 23
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=69.28 E-value=12 Score=22.07 Aligned_cols=25 Identities=36% Similarity=0.521 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhccC
Q psy648 48 LAVLNEKLTTLERRIEYLEARKSHG 72 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAklss~ 72 (72)
+..|+-+|..++..+..++.+|+.+
T Consensus 6 ~~rL~Kel~kl~~~i~~~~~kL~n~ 30 (66)
T PF10458_consen 6 IERLEKELEKLEKEIERLEKKLSNE 30 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCST
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 5678888899999999999888763
No 24
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=68.88 E-value=24 Score=22.46 Aligned_cols=38 Identities=34% Similarity=0.508 Sum_probs=19.2
Q ss_pred hHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 29 SIKKITDFLNSFDM---SCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 29 ~I~~~~~FLN~F~~---sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
.+..|-++++.... +|......++.+++.|+.++.-|.
T Consensus 59 sl~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~ 99 (123)
T cd04770 59 SLAEIRELLSLRDDGAAPCAEVRALLEEKLAEVEAKIAELQ 99 (123)
T ss_pred CHHHHHHHHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666665432 344444555555555555444443
No 25
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=68.54 E-value=15 Score=23.28 Aligned_cols=39 Identities=33% Similarity=0.453 Sum_probs=17.6
Q ss_pred hHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 29 SIKKITDFLNSF---DMSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 29 ~I~~~~~FLN~F---~~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
.+..|-++|+.- +.+|.....-+..+++.|++++.-|+.
T Consensus 59 sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (113)
T cd01109 59 SIKDIKEYAELRREGDSTIPERLELLEEHREELEEQIAELQE 100 (113)
T ss_pred CHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555432 123444444444444444444444443
No 26
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=67.90 E-value=12 Score=21.82 Aligned_cols=22 Identities=23% Similarity=0.383 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhhc
Q psy648 49 AVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 49 a~ln~KL~~LE~~L~~LEAkls 70 (72)
+.|.+++..||.+|..|++.++
T Consensus 2 ~aLrqQv~aL~~qv~~Lq~~fs 23 (46)
T PF09006_consen 2 NALRQQVEALQGQVQRLQAAFS 23 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 5678888888888888888765
No 27
>PF07195 FliD_C: Flagellar hook-associated protein 2 C-terminus; InterPro: IPR010809 The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria []. This alignment covers the C-terminal region of the flagellar hook-associated protein 2.; GO: 0007155 cell adhesion, 0009288 bacterial-type flagellum
Probab=66.37 E-value=42 Score=23.90 Aligned_cols=30 Identities=30% Similarity=0.357 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 41 DMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..+-...+..++.++..+|++++-.|+++.
T Consensus 195 ~~~l~~~~~~~~~~i~~~~~rl~~~~~~l~ 224 (239)
T PF07195_consen 195 IDSLNSQIKSLDKQIEDLEERLESKEERLR 224 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566677777777777777777766653
No 28
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=65.67 E-value=25 Score=23.43 Aligned_cols=25 Identities=16% Similarity=0.185 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..|++.+++++..|++....|+..+
T Consensus 85 ~~~~~~l~~~i~~L~~~~~~L~~~~ 109 (135)
T PRK10227 85 LEKVAEIERHIEELQSMRDQLLALA 109 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666666666666666666544
No 29
>PRK09458 pspB phage shock protein B; Provisional
Probab=64.51 E-value=18 Score=22.98 Aligned_cols=29 Identities=38% Similarity=0.407 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
.=+.+|.+|-++-++++.+++.||.=|.+
T Consensus 39 ~d~~~L~~L~~~A~rm~~RI~tLE~ILDa 67 (75)
T PRK09458 39 EEQQRLAQLTEKAERMRERIQALEAILDA 67 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 34678999999999999999999987654
No 30
>PLN02281 chlorophyllide a oxygenase
Probab=63.98 E-value=30 Score=28.76 Aligned_cols=57 Identities=30% Similarity=0.413 Sum_probs=47.0
Q ss_pred hhhHHHHHHHHHHHhHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 15 QDWANREYIEIITGSIKKITDFLNSFDM------SCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 15 ~DW~nRe~i~~in~~I~~~~~FLN~F~~------sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
-||.-|.=+-.|-..=-+.|+-||-..- +-+.-|+.|.+.|.+.-.++-+=||+|++
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 153 (536)
T PLN02281 91 LDWRARQDLLTIMILHDKVVDVLNPLAREYKSIGTVKKELAGLQEELSKAHQQVHISEARVST 153 (536)
T ss_pred ccchhhhhHHHHHHHhHHHHHHhhhHHHhhhhHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHH
Confidence 4999998766666666788999996653 45678999999999999999999999975
No 31
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=63.89 E-value=18 Score=22.62 Aligned_cols=28 Identities=36% Similarity=0.354 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
=+.+|..|.++-+++|.+++.||.=|..
T Consensus 40 d~~~L~~L~~~a~rm~eRI~tLE~ILda 67 (75)
T PF06667_consen 40 DEQRLQELYEQAERMEERIETLERILDA 67 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 3678999999999999999999987654
No 32
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=63.89 E-value=24 Score=23.53 Aligned_cols=40 Identities=23% Similarity=0.397 Sum_probs=23.0
Q ss_pred HHhHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 27 TGSIKKITDFLNSFD----MSCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 27 n~~I~~~~~FLN~F~----~sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
...+..|.+||+... ..|....+.++.+++.+++++.-|+
T Consensus 58 G~sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 101 (140)
T PRK09514 58 GFTLEEIRELLSIRLDPEHHTCQEVKGIVDEKLAEVEAKIAELQ 101 (140)
T ss_pred CCCHHHHHHHHHhcccCCcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667777776431 2465555666666666666555544
No 33
>PF14965 BRI3BP: Negative regulator of p53/TP53
Probab=63.86 E-value=3.2 Score=30.12 Aligned_cols=36 Identities=31% Similarity=0.367 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 34 TDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 34 ~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
+-||-....+-..+ ..+++|+..||++++.||-+.+
T Consensus 141 ~~~l~g~~gs~~~~-~~LE~kv~~LE~qvr~L~~R~~ 176 (177)
T PF14965_consen 141 VCFLTGLVGSYWRS-ASLEAKVRHLERQVRELNIRQR 176 (177)
T ss_pred HHHHccccCCCCCc-ccHHHHHHHHHHHHHHHHHHhc
Confidence 33454554444444 8899999999999999997764
No 34
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=62.91 E-value=13 Score=23.36 Aligned_cols=23 Identities=17% Similarity=0.449 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Q psy648 48 LAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkls 70 (72)
+..++.||+.+|.++++-.|.+.
T Consensus 14 ~~~i~~rLd~iEeKvEf~~~Ei~ 36 (70)
T PF04210_consen 14 FNEIMKRLDEIEEKVEFTNAEIA 36 (70)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHH
Confidence 46788999999999999888764
No 35
>PF10241 KxDL: Uncharacterized conserved protein; InterPro: IPR019371 This entry represents a conserved region of 80 residues which defines a family of short proteins. There is a characteristic KxDL motif towards the C terminus. The function is unknown.
Probab=62.85 E-value=35 Score=21.31 Aligned_cols=53 Identities=19% Similarity=0.298 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 18 ANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 18 ~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
.|++...+....-.+...+-.+|...++. +..+..-|+.+-+++..|.++++.
T Consensus 30 tn~~L~~~n~~s~~rl~~~~~~f~~~~~~-l~~mK~DLd~i~krir~lk~kl~~ 82 (88)
T PF10241_consen 30 TNEELLNLNDLSQQRLAEARERFARHTKL-LKEMKKDLDYIFKRIRSLKAKLAK 82 (88)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58899999989999999999999988865 677888999999999999998864
No 36
>PRK04406 hypothetical protein; Provisional
Probab=62.36 E-value=16 Score=22.63 Aligned_cols=19 Identities=26% Similarity=0.517 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q psy648 50 VLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 50 ~ln~KL~~LE~~L~~LEAk 68 (72)
.+++||..||.++.+.|.-
T Consensus 8 ~le~Ri~~LE~~lAfQE~t 26 (75)
T PRK04406 8 QLEERINDLECQLAFQEQT 26 (75)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4666666666666666543
No 37
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=62.28 E-value=37 Score=21.97 Aligned_cols=40 Identities=20% Similarity=0.348 Sum_probs=19.5
Q ss_pred HhHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 28 GSIKKITDFLNSFDM------SCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 28 ~~I~~~~~FLN~F~~------sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
..+..|-++++..+. .|+..+..+.++++.|+.++.-|++
T Consensus 56 ~~L~~I~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~l~~ 101 (118)
T cd04776 56 FSLEEIRELLDLYDPPGGNRKQLEKMLEKIEKRRAELEQQRRDIDA 101 (118)
T ss_pred CCHHHHHHHHHhhccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666665432 2344444455555555544444443
No 38
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=62.03 E-value=31 Score=21.76 Aligned_cols=32 Identities=28% Similarity=0.406 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 39 SFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 39 ~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
......+.++..++++++.++.....|+..+.
T Consensus 75 ~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~l~ 106 (108)
T cd01107 75 ELRKLLREKLAELEAEIEELQRILRLLEDRLK 106 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44556778888888888888888888887664
No 39
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=61.66 E-value=20 Score=23.24 Aligned_cols=41 Identities=22% Similarity=0.382 Sum_probs=22.9
Q ss_pred hHHHHHHHHHHH---HHHH-------HHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 29 SIKKITDFLNSF---DMSC-------RSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 29 ~I~~~~~FLN~F---~~sc-------~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.+..|-++|+-. +.+| ..|++.+++++..|......|+..+
T Consensus 59 sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~ 109 (127)
T TIGR02044 59 SLEECKELLNLWNDPNRTSADVKARTLEKVAEIERKISELQSMRDQLEALA 109 (127)
T ss_pred CHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455566666533 2234 3456666666666666666666554
No 40
>PF05480 Staph_haemo: Staphylococcus haemolytic protein; InterPro: IPR008846 This family consists of several different short Staphylococcal proteins, it contains SLUSH A, B and C proteins as well as haemolysin and gonococcal growth inhibitor. Some strains of the coagulase-negative Staphylococcus lugdunensis produce a synergistic hemolytic activity (SLUSH), phenotypically similar to the delta-hemolysin of S. aureus []. Gonococcal growth inhibitor from Staphylococcus acts on the cytoplasmic membrane of the gonococcal cell causing cytoplasmic leakage and, eventually, death [].; GO: 0009405 pathogenesis
Probab=61.35 E-value=29 Score=19.92 Aligned_cols=34 Identities=24% Similarity=0.423 Sum_probs=24.5
Q ss_pred hHHHHHHHHHhhhHHHHHHHHHHHhHHHHHHHHHHH
Q psy648 5 HREAIQKQIQQDWANREYIEIITGSIKKITDFLNSF 40 (72)
Q Consensus 5 ~~~~v~~~iq~DW~nRe~i~~in~~I~~~~~FLN~F 40 (72)
-...|+..+.+||.. +-.-|-.-+.+-++++.+|
T Consensus 8 I~n~V~Ag~~~Dwa~--lgtsIv~iv~ngv~~i~k~ 41 (43)
T PF05480_consen 8 IKNTVQAGQNQDWAK--LGTSIVDIVENGVDIISKF 41 (43)
T ss_pred HHHHHHHHHhccHHH--HHHHHHHHHHHHHHHHHHH
Confidence 467899999999985 4445555566667777665
No 41
>PF03105 SPX: SPX domain; InterPro: IPR004331 The SPX domain is named after SYG1/Pho81/XPR1 proteins. This 180 residue length domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1, the N terminus directly binds to the G- protein beta subunit and inhibits transduction of the mating pheromone signal [] suggesting that all the members of this family are involved in G-protein associated signal transduction. The C-terminal of these proteins often have an EXS domain (IPR004342 from INTERPRO) []. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family [, ]. NUC-2 contains several ankyrin repeats (IPR002110 from INTERPRO). Several members of this family are the XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with Murine leukemia virus (MLV) []. The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae [, ]. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction [, , ] and may itself function as a phosphate sensor [].
Probab=61.27 E-value=49 Score=22.48 Aligned_cols=43 Identities=26% Similarity=0.576 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 18 ANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 18 ~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
...+|...+..-+.++-+|-. .|...+.+++..|+.++..++.
T Consensus 92 ~~~~F~~~L~~El~KVn~Fy~-------~k~~el~~~~~~L~~ql~~l~~ 134 (275)
T PF03105_consen 92 SEEEFFELLDEELEKVNDFYK-------EKEKELRERLEELQKQLEELRE 134 (275)
T ss_pred hHHHHHHhhHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHh
Confidence 678899999999999988865 5666666666666666666544
No 42
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=61.20 E-value=15 Score=21.99 Aligned_cols=17 Identities=35% Similarity=0.376 Sum_probs=6.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy648 46 SRLAVLNEKLTTLERRI 62 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L 62 (72)
.||..|+.||.-.|..+
T Consensus 4 ~Ri~~LE~~la~qe~~i 20 (69)
T PF04102_consen 4 ERIEELEIKLAFQEDTI 20 (69)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34444444443333333
No 43
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=61.08 E-value=30 Score=23.81 Aligned_cols=40 Identities=20% Similarity=0.239 Sum_probs=22.7
Q ss_pred HhHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 28 GSIKKITDFLNSFD----MSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 28 ~~I~~~~~FLN~F~----~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
..+..|.+||+.+. .+|....+-++++++.+++++.-|.+
T Consensus 68 ~sL~eIk~ll~~~~~~~~~~~~~~~~ll~~k~~~l~~~I~~L~~ 111 (154)
T PRK15002 68 IPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVA 111 (154)
T ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777777542 34555555555555555555555443
No 44
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=59.95 E-value=40 Score=21.01 Aligned_cols=40 Identities=25% Similarity=0.334 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 31 KKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 31 ~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
-...+||++=-...+..+..++.++..+..++..+++.++
T Consensus 76 ~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~ 115 (120)
T PF02996_consen 76 EEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQ 115 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456677666666677777777777777777777666553
No 45
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=59.63 E-value=22 Score=22.49 Aligned_cols=29 Identities=17% Similarity=0.311 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 42 MSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..-+.++..+++++..|++.+..|+-++.
T Consensus 82 ~~l~~~~~~l~~~i~~l~~~~~~l~~~~~ 110 (113)
T cd01109 82 ELLEEHREELEEQIAELQETLAYLDYKID 110 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44578899999999999999999887764
No 46
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=59.51 E-value=22 Score=22.68 Aligned_cols=30 Identities=23% Similarity=0.286 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 41 DMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
....+.|+..+++++..|......|+..++
T Consensus 83 ~~~l~~~~~~l~~~i~~L~~~~~~L~~~l~ 112 (112)
T cd01282 83 LAVLRRELARIDRQIADLTRSRDRLDAYLA 112 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 456689999999999999999999998764
No 47
>PF08702 Fib_alpha: Fibrinogen alpha/beta chain family; InterPro: IPR012290 Fibrinogen plays key roles in both blood clotting and platelet aggregation. During blood clot formation, the conversion of soluble fibrinogen to insoluble fibrin is triggered by thrombin, resulting in the polymerisation of fibrin, which forms a soft clot; this is then converted to a hard clot by factor XIIIA, which cross-links fibrin molecules. Platelet aggregation involves the binding of the platelet protein receptor integrin alpha(IIb)-beta(3) to the C-terminal D domain of fibrinogen []. In addition to platelet aggregation, platelet-fibrinogen interaction mediates both adhesion and fibrin clot retraction. Fibrinogen occurs as a dimer, where each monomer is composed of three non-identical chains, alpha, beta and gamma, linked together by several disulphide bonds []. The N-terminals of all six chains come together to form the centre of the molecule (E domain), from which the monomers extend in opposite directions as coiled coils, followed by C-terminal globular domains (D domains). Therefore, the domain composition is: D-coil-E-coil-D. At each end, the C-terminal of the alpha chain extends beyond the D domain as a protuberance that is important for cross-linking the molecule. During clot formation, the N-terminal fragments of the alpha and beta chains (within the E domain) in fibrinogen are cleaved by thrombin, releasing fibrinopeptides A and B, respectively, and producing fibrin. This cleavage results in the exposure of four binding sites on the E domain, each of which can bind to a D domain from different fibrin molecules. The binding of fibrin molecules produces a polymer consisting of a lattice network of fibrins that form a long, branching, flexible fibre [, ]. Fibrin fibres interact with platelets to increase the size of the clot, as well as with several different proteins and cells, thereby promoting the inflammatory response and concentrating the cells required for wound repair at the site of damage. This entry represents the coiled-coil domain and part of the N-terminal E domain found in all three fibrinogen polypeptides, namely the alpha, beta and gamma chains. More information about these proteins can be found at Protein of the Month: Fibrinogen [].; GO: 0005102 receptor binding, 0030674 protein binding, bridging, 0007165 signal transduction, 0030168 platelet activation, 0051258 protein polymerization, 0005577 fibrinogen complex; PDB: 1LWU_D 1N73_D 1M1J_B 1JY2_R 1JY3_R 1RF0_A 2H43_D 1RE4_D 2XNY_D 2HPC_D ....
Probab=59.16 E-value=32 Score=23.55 Aligned_cols=30 Identities=20% Similarity=0.429 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 32 KITDFLNSFDMSCRSRLAVLNEKLTTLERR 61 (72)
Q Consensus 32 ~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~ 61 (72)
.+.+||++++..-..+|..|+..|..++.+
T Consensus 22 ~i~~~L~k~~~~v~~~i~~L~~~L~~~~n~ 51 (146)
T PF08702_consen 22 GIQDFLDKYERDVDKDIQELENLLDQISNS 51 (146)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHccchHHHHHHHHHHHHHHHHh
Confidence 367888888888888888888888877764
No 48
>PRK09343 prefoldin subunit beta; Provisional
Probab=59.15 E-value=21 Score=23.48 Aligned_cols=25 Identities=24% Similarity=0.341 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
+.|+..++.+|..||.+..+|+.++
T Consensus 77 ~~r~E~ie~~ik~lekq~~~l~~~l 101 (121)
T PRK09343 77 KERKELLELRSRTLEKQEKKLREKL 101 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444444443
No 49
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=58.87 E-value=18 Score=18.32 Aligned_cols=17 Identities=24% Similarity=0.526 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy648 48 LAVLNEKLTTLERRIEY 64 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~ 64 (72)
+..+-.|+..||++|.+
T Consensus 3 ~~rlr~rI~dLer~L~~ 19 (23)
T PF04508_consen 3 MNRLRNRISDLERQLSE 19 (23)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34566777788888765
No 50
>PF08657 DASH_Spc34: DASH complex subunit Spc34 ; InterPro: IPR013966 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=58.63 E-value=20 Score=26.82 Aligned_cols=28 Identities=32% Similarity=0.583 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..++|++.|-.+-+.|..++.+||++|+
T Consensus 177 ga~eki~~Lr~~y~~l~~~i~~lE~~Va 204 (259)
T PF08657_consen 177 GAREKIAALRQRYNQLSNSIAYLEAEVA 204 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5578999999999999999999999885
No 51
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=58.11 E-value=18 Score=25.62 Aligned_cols=29 Identities=24% Similarity=0.346 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 42 MSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..+..+++-|+++++.++.++.-||..++
T Consensus 81 ~t~~~R~~lLe~~~~~l~~ri~eLe~~l~ 109 (175)
T PRK13182 81 NISSVDFEQLEAQLNTITRRLDELERQLQ 109 (175)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777777777777777777776653
No 52
>PRK02119 hypothetical protein; Provisional
Probab=58.01 E-value=17 Score=22.30 Aligned_cols=16 Identities=31% Similarity=0.657 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHHHHH
Q psy648 51 LNEKLTTLERRIEYLE 66 (72)
Q Consensus 51 ln~KL~~LE~~L~~LE 66 (72)
+++||..||.++.+.|
T Consensus 7 ~e~Ri~~LE~rla~QE 22 (73)
T PRK02119 7 LENRIAELEMKIAFQE 22 (73)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4444444444444444
No 53
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=57.96 E-value=20 Score=24.41 Aligned_cols=26 Identities=31% Similarity=0.418 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
+.|+.+|+-|+.+||++-+.++-++.
T Consensus 76 ~er~E~Le~ri~tLekQe~~l~e~l~ 101 (119)
T COG1382 76 EERKETLELRIKTLEKQEEKLQERLE 101 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666777666666665553
No 54
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=57.57 E-value=26 Score=20.92 Aligned_cols=24 Identities=25% Similarity=0.324 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
+.|+..++++++.+|+....+|.+
T Consensus 12 e~~l~~~~~~i~~lE~~~~~~e~~ 35 (71)
T PF10779_consen 12 ETKLDNHEERIDKLEKRDAANEKD 35 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555555555555555544
No 55
>PF05278 PEARLI-4: Arabidopsis phospholipase-like protein (PEARLI 4); InterPro: IPR007942 This family contains several phospholipase-like proteins from Arabidopsis thaliana and other members of the Streptophyta which are homologous to PEARLI 4.
Probab=57.44 E-value=43 Score=25.65 Aligned_cols=40 Identities=18% Similarity=0.350 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 31 KKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 31 ~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
..+.++-.++. -|+.||+.++.+-.+|+.++.++..||.+
T Consensus 221 ke~~e~~~~i~-e~~~rl~~l~~~~~~l~k~~~~~~sKV~k 260 (269)
T PF05278_consen 221 KEVKEIKERIT-EMKGRLGELEMESTRLSKTIKSIKSKVEK 260 (269)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556666774 89999999999999999999999988853
No 56
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=57.09 E-value=26 Score=22.30 Aligned_cols=25 Identities=24% Similarity=0.343 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
-++.|++.+..||-.||++..-+|.
T Consensus 12 K~k~Kiae~Q~rlK~Le~qk~E~EN 36 (83)
T PF14193_consen 12 KTKEKIAELQARLKELEAQKTEAEN 36 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999998877764
No 57
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=56.85 E-value=34 Score=19.20 Aligned_cols=39 Identities=38% Similarity=0.577 Sum_probs=25.7
Q ss_pred hHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 29 SIKKITDFLNS---FDMSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 29 ~I~~~~~FLN~---F~~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
.+..|-+||.- =+..|.....-+.+|+..++.++.-|.+
T Consensus 16 sL~eI~~~l~l~~~~~~~~~~~~~~l~~~~~~i~~~i~~L~~ 57 (65)
T PF09278_consen 16 SLEEIRELLELYDQGDPPCADRRALLEEKLEEIEEQIAELQA 57 (65)
T ss_dssp -HHHHHHHHHHCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHhccCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666622 1457777778888888888888777664
No 58
>PRK02793 phi X174 lysis protein; Provisional
Probab=56.74 E-value=16 Score=22.25 Aligned_cols=16 Identities=38% Similarity=0.711 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHH
Q psy648 51 LNEKLTTLERRIEYLE 66 (72)
Q Consensus 51 ln~KL~~LE~~L~~LE 66 (72)
++.||..||-++.+.|
T Consensus 6 ~e~Ri~~LE~~lafQe 21 (72)
T PRK02793 6 LEARLAELESRLAFQE 21 (72)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444444444
No 59
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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. This subgroup lacks one of the c
Probab=56.26 E-value=54 Score=21.40 Aligned_cols=43 Identities=21% Similarity=0.234 Sum_probs=25.3
Q ss_pred HHhHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 27 TGSIKKITDFLNSFD----------MSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 27 n~~I~~~~~FLN~F~----------~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
...+..|-++|...+ ..-+.|++.+++++..|.+.+..|+.++
T Consensus 57 G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~ 109 (133)
T cd04787 57 GFSLKDIKEILSHADQGESPCPMVRRLIEQRLAETERRIKELLKLRDRMQQAV 109 (133)
T ss_pred CCCHHHHHHHHhhhccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566666666543 2235666666666666666666666554
No 60
>PF05531 NPV_P10: Nucleopolyhedrovirus P10 protein; InterPro: IPR008702 This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra [].; GO: 0019028 viral capsid
Probab=56.07 E-value=49 Score=20.87 Aligned_cols=23 Identities=22% Similarity=0.364 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Q psy648 48 LAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkls 70 (72)
...++.||+.+.++|+-|+.+|+
T Consensus 37 v~~l~~klDa~~~~l~~l~~~V~ 59 (75)
T PF05531_consen 37 VTELNKKLDAQSAQLTTLNTKVN 59 (75)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 34466666666666666666654
No 61
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, 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=55.59 E-value=28 Score=21.11 Aligned_cols=40 Identities=45% Similarity=0.585 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 29 SIKKITDFLNSFDM--SCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 29 ~I~~~~~FLN~F~~--sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
.+..+..++...+. +|......+..++..|++++..|.+.
T Consensus 58 ~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~ 99 (100)
T cd00592 58 SLKEIRELLDARDEELSLAALLALLDEKLAELEEKIARLEAL 99 (100)
T ss_pred CHHHHHHHHhcccccchHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 33444444433332 27889999999999999999988764
No 62
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=55.45 E-value=51 Score=20.85 Aligned_cols=36 Identities=14% Similarity=0.261 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 33 ITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 33 ~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
+..+++....-. ..|..+-.+|+.+|.++.-||+-+
T Consensus 47 l~~~~~~l~~k~-~~l~~~l~~Id~Ie~~V~~LE~~v 82 (99)
T PF10046_consen 47 LEKNLEDLNQKY-EELQPYLQQIDQIEEQVTELEQTV 82 (99)
T ss_pred HHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444443322 233334444445555665555543
No 63
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=55.11 E-value=26 Score=20.92 Aligned_cols=23 Identities=35% Similarity=0.540 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
++|+.+.+.|+..++..++-||-
T Consensus 5 ~e~l~~ie~~l~~~~~~i~~lE~ 27 (71)
T PF10779_consen 5 KEKLNRIETKLDNHEERIDKLEK 27 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555555555544
No 64
>PRK08032 fliD flagellar capping protein; Reviewed
Probab=54.95 E-value=77 Score=25.09 Aligned_cols=31 Identities=16% Similarity=0.138 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 40 FDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 40 F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
...+-...+..++.++..+|++|+-+|.++.
T Consensus 407 ~~~~l~~~i~~l~~~i~~~~~rl~~~e~rl~ 437 (462)
T PRK08032 407 ATDGVNKTLKKLTKQYNAVSDSIDATIARYK 437 (462)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445666777788888888888877777653
No 65
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=54.65 E-value=37 Score=21.99 Aligned_cols=25 Identities=24% Similarity=0.248 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
+.|++.+++++..|++....|+..+
T Consensus 82 ~~~~~~l~~~i~~L~~~~~~L~~~~ 106 (124)
T TIGR02051 82 SRKLKSVQAKMADLLRIERLLEELL 106 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666666666655665543
No 66
>KOG3501|consensus
Probab=54.57 E-value=33 Score=23.38 Aligned_cols=46 Identities=17% Similarity=0.221 Sum_probs=33.7
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 22 YIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 22 ~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
|-...+.|++.- +-.-.+.-+.|+...++++..|+.+-.|||-.++
T Consensus 53 Y~svgrmF~l~d---k~a~~s~leak~k~see~IeaLqkkK~YlEk~v~ 98 (114)
T KOG3501|consen 53 YTSVGRMFMLSD---KAAVRSHLEAKMKSSEEKIEALQKKKTYLEKTVS 98 (114)
T ss_pred HHHHHHHHHcCc---HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 444555555432 2234567788999999999999999999998775
No 67
>PF15112 DUF4559: Domain of unknown function (DUF4559)
Probab=54.52 E-value=1e+02 Score=24.12 Aligned_cols=50 Identities=16% Similarity=0.299 Sum_probs=39.4
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 20 REYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 20 Re~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
+..++.+-.|+..=-|-.+.|..-- .||..|..|++++|..+.-++.++.
T Consensus 256 ~~~l~~~~~fL~~NkDL~~~l~~e~-qkL~~l~~k~~~~~~~v~~~~~~~~ 305 (307)
T PF15112_consen 256 SKRLEVLKEFLRNNKDLRSNLQEEL-QKLDSLQTKHQKLESDVKELKSQMP 305 (307)
T ss_pred hHHHHHHHHHHHhcHHHHHHHHHHH-HHHHHHHHHhcchhhhhhHHHhhcc
Confidence 5666777777777777777887666 8999999999999998888877653
No 68
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=53.75 E-value=58 Score=21.04 Aligned_cols=40 Identities=28% Similarity=0.329 Sum_probs=20.3
Q ss_pred HhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 28 GSIKKITDFLNSFD---MSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 28 ~~I~~~~~FLN~F~---~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
..+..|-+++.... ..|.....-+..+++.+|.++.-|++
T Consensus 58 ~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (126)
T cd04785 58 FSLEEIRALLALSDRPDRSCAEADAIARAHLADVRARIADLRR 100 (126)
T ss_pred CCHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666665433 23444455555555555555554443
No 69
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=53.40 E-value=53 Score=21.39 Aligned_cols=39 Identities=31% Similarity=0.436 Sum_probs=18.6
Q ss_pred HhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 28 GSIKKITDFLNSFD---MSCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 28 ~~I~~~~~FLN~F~---~sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
..+..|-++|...+ .+|......+..+++.||+++.-|+
T Consensus 58 ~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T TIGR02047 58 MSLAEIRQLLRYQDKPEKSCSDVNALLDEHISHVRARIIKLQ 99 (127)
T ss_pred CCHHHHHHHHHhhhCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556666665432 2344444444444444444444443
No 70
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=53.36 E-value=35 Score=28.11 Aligned_cols=33 Identities=24% Similarity=0.390 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 35 DFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 35 ~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
-+++-|....-.-+..+. ||+.|+++|+-|+++
T Consensus 14 l~~s~~~~a~~~~~~~~q-kie~L~kql~~Lk~q 46 (489)
T PF11853_consen 14 LFLSLPAAAMADDIDLLQ-KIEALKKQLEELKAQ 46 (489)
T ss_pred HHhccchhhhhhhhHHHH-HHHHHHHHHHHHHHh
Confidence 445544444444333333 444445555444444
No 71
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=52.64 E-value=47 Score=21.76 Aligned_cols=39 Identities=23% Similarity=0.420 Sum_probs=19.7
Q ss_pred HhHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 28 GSIKKITDFLNSF----DMSCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 28 ~~I~~~~~FLN~F----~~sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
..+..|.++++.. +.+|....+.+..+++.|+.++.-|+
T Consensus 59 ~sl~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 101 (131)
T TIGR02043 59 FTLDEIKELLSIKLDATEHSCAEVKAIVDAKLELVDEKINELT 101 (131)
T ss_pred CCHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566667777643 12454444445555555554444443
No 72
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=52.52 E-value=26 Score=21.80 Aligned_cols=14 Identities=36% Similarity=0.527 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHH
Q psy648 51 LNEKLTTLERRIEY 64 (72)
Q Consensus 51 ln~KL~~LE~~L~~ 64 (72)
|+..|..||.+|=-
T Consensus 14 Le~~L~~lE~qIy~ 27 (80)
T PF09340_consen 14 LEKDLAALEKQIYD 27 (80)
T ss_pred HHHHHHHHHHHHHH
Confidence 33444444444433
No 73
>PF14084 DUF4264: Protein of unknown function (DUF4264)
Probab=52.44 E-value=8.1 Score=23.03 Aligned_cols=10 Identities=50% Similarity=0.886 Sum_probs=8.3
Q ss_pred HHHHHHHHHH
Q psy648 30 IKKITDFLNS 39 (72)
Q Consensus 30 I~~~~~FLN~ 39 (72)
+-++|||||+
T Consensus 16 lYKvVDfLNk 25 (52)
T PF14084_consen 16 LYKVVDFLNK 25 (52)
T ss_pred HHHHHHHHhh
Confidence 4589999997
No 74
>PF11945 WASH_WAHD: WAHD domain of WASH complex; InterPro: IPR021854 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. This entry represents the WASH subunit of the WASH complex. WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires probably vary extensively among individuals []. It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7 transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene.
Probab=51.81 E-value=95 Score=23.77 Aligned_cols=20 Identities=25% Similarity=0.537 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy648 45 RSRLAVLNEKLTTLERRIEY 64 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~ 64 (72)
+.||..+++|+..+.++++.
T Consensus 49 ~~~l~~i~~Ri~~~qaKi~~ 68 (297)
T PF11945_consen 49 RERLQAIQQRIEVAQAKIEK 68 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 44444444444444444443
No 75
>KOG3684|consensus
Probab=51.80 E-value=62 Score=26.91 Aligned_cols=49 Identities=22% Similarity=0.364 Sum_probs=27.2
Q ss_pred hhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 16 DWANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 16 DW~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.|++|.+-+-.|.+.- +-+-.+...+.+.+++.+=+.+|.+++.||-|+
T Consensus 409 k~~qRkl~e~~nsl~d-----~aK~~~~myd~~~~l~~~q~~le~qI~~Le~kl 457 (489)
T KOG3684|consen 409 KWEQRKLSEQANSLVD-----LAKTQNDMYDLLQELHSRQEELEKQIDTLESKL 457 (489)
T ss_pred HHHHHHHHhhcccHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6888888877665532 222333444555555555555555555555554
No 76
>TIGR02132 phaR_Bmeg polyhydroxyalkanoic acid synthase, PhaR subunit. This model describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit.
Probab=51.50 E-value=96 Score=22.84 Aligned_cols=62 Identities=13% Similarity=0.180 Sum_probs=37.2
Q ss_pred HHHHHHHhhhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHhh
Q psy648 8 AIQKQIQQDWANREYIEIITGSIKKITDFLNSFDMSCRSRL-----------AVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 8 ~v~~~iq~DW~nRe~i~~in~~I~~~~~FLN~F~~sc~~kL-----------a~ln~KL~~LE~~L~~LEAkl 69 (72)
.+.+.+.+-=+.-||.+.|..-.--......-|..+++..| +++-..+..||-+++-||..+
T Consensus 23 ~wak~~~q~m~TEEFSa~IG~vLd~yL~yQKafnE~MekYLe~lNlPSr~DiarvA~lvinlE~kvD~lee~f 95 (189)
T TIGR02132 23 FWGKAIGDNIKREEFSALMGNVLDLNLFYQKALNDTTGNYLEQVNVPTKEDIANVASLVINLEEKVDLIEEFF 95 (189)
T ss_pred HHHHHHHHHHchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444556666665555444455555555555544 555677888888888888765
No 77
>cd05511 Bromo_TFIID Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine.
Probab=51.00 E-value=36 Score=21.95 Aligned_cols=25 Identities=36% Similarity=0.328 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 38 NSFDMSCRSRLAVLNEKLTTLERRI 62 (72)
Q Consensus 38 N~F~~sc~~kLa~ln~KL~~LE~~L 62 (72)
..-...|+.++..++++|..||+.+
T Consensus 87 ~~l~~~~~~~~~~~~~~~~~~~~~~ 111 (112)
T cd05511 87 KEMLELAEELLAEREEKLTQLEKNI 111 (112)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHhc
Confidence 3456678888888888888888865
No 78
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=50.98 E-value=33 Score=21.61 Aligned_cols=41 Identities=12% Similarity=0.128 Sum_probs=23.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 29 SIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 29 ~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..-.+...|+.=-..++.++..++.++..++..+.-+++++
T Consensus 60 ~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk~~l 100 (105)
T cd00632 60 EKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQEKI 100 (105)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445555555555566666666666666666666665554
No 79
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=50.95 E-value=51 Score=21.21 Aligned_cols=40 Identities=28% Similarity=0.447 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHH-HH-------HHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 30 IKKITDFLNSFDM-SC-------RSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 30 I~~~~~FLN~F~~-sc-------~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
+..|-++|+..+. .| +.|+..+++++..|+.....|+..+
T Consensus 60 L~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~l~~~~ 107 (126)
T cd04783 60 LDEIAELLELDDGTDCSEARELAEQKLAEVDEKIADLQRMRASLQELV 107 (126)
T ss_pred HHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555554321 23 4566666666666666666666544
No 80
>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Probab=50.52 E-value=71 Score=21.06 Aligned_cols=63 Identities=16% Similarity=0.162 Sum_probs=50.6
Q ss_pred HHHHHHHhhhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 8 AIQKQIQQDWANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 8 ~v~~~iq~DW~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
++-...+.|=..||-+.--.+-+..-.+-|+..-...+.+++.++.++..++.+..-++.++.
T Consensus 42 ~Ll~~~~r~~~~~e~l~~~~~~l~~d~~~l~~~~~rL~~~~~~~ere~~~~~~~~~~l~~~~~ 104 (151)
T PF11559_consen 42 DLLQQRDRDMEQREDLSDKLRRLRSDIERLQNDVERLKEQLEELERELASAEEKERQLQKQLK 104 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667888888888888888888888888888888888888888888888777777776654
No 81
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=49.90 E-value=35 Score=23.51 Aligned_cols=18 Identities=22% Similarity=0.475 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHhhccC
Q psy648 55 LTTLERRIEYLEARKSHG 72 (72)
Q Consensus 55 L~~LE~~L~~LEAklss~ 72 (72)
+...+++|++|+.++.+|
T Consensus 67 ~~D~~KRL~iLfd~ln~g 84 (157)
T PF07304_consen 67 VDDIEKRLNILFDHLNNG 84 (157)
T ss_dssp HHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHhcC
Confidence 466777777777766543
No 82
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=49.78 E-value=69 Score=22.91 Aligned_cols=42 Identities=19% Similarity=0.377 Sum_probs=26.3
Q ss_pred HHhHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHh
Q psy648 27 TGSIKKITDFLNSFDMSCR-------------SRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 27 n~~I~~~~~FLN~F~~sc~-------------~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
..-+-.++.||-++...-. .-++.|..++..||..+.-|+.+
T Consensus 79 ~ltl~~vI~fLq~l~~~~~~~~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~ 133 (161)
T TIGR02894 79 SLTLQDVISFLQNLKTTNPSDQALQKENERLKNQNESLQKRNEELEKELEKLRQR 133 (161)
T ss_pred cCCHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4557889999999986422 33455555555566555555544
No 83
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=49.70 E-value=25 Score=21.07 Aligned_cols=21 Identities=19% Similarity=0.374 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q psy648 48 LAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAk 68 (72)
+..++.++.+++.+++-+.+.
T Consensus 2 i~elEn~~~~~~~~i~tvk~e 22 (55)
T PF05377_consen 2 IDELENELPRIESSINTVKKE 22 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555555555443
No 84
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=49.13 E-value=65 Score=20.22 Aligned_cols=29 Identities=24% Similarity=0.395 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 42 MSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
...+.++..++.++..++.++..++.++.
T Consensus 66 ~~Le~~~e~le~~i~~l~~~~~~l~~~~~ 94 (105)
T cd00632 66 TELKERLETIELRIKRLERQEEDLQEKLK 94 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566667777777777777777776654
No 85
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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 dissimil
Probab=49.12 E-value=42 Score=20.99 Aligned_cols=28 Identities=25% Similarity=0.288 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 42 MSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..-..++..+++++..|+..+..|+.-|
T Consensus 74 ~~l~~~~~~l~~~i~~l~~~~~~l~~~l 101 (102)
T cd04775 74 AILEERLQSLNREIQRLRQQQQVLAAIL 101 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4456777778888888888877777654
No 86
>PF12699 phiKZ_IP: phiKZ-like phage internal head proteins; InterPro: IPR024413 Phage internal head proteins (IP) are proteins that are encoded by a bacteriophage and assembled into the mature virion inside the capsid head. The most analogous characterised IP proteins are those of bacteriophage T4, which are known to be proteolytically processed during phage maturation, and then subsequently injected into the host cell during infection. The phiKZ_IP family consists of internal head proteins encoded by phiKZ-like phages. Each phage encodes three to six members of this family []. Members of the family reside in the head [] and are cleaved during phage maturation to separate an N-terminal propeptide from a C-terminal domain. The C-terminal domain remains in the mature capsid. The N-terminal propeptide domain is either mostly or completely removed from the mature capsid. In one case, an unrelated polypeptide is embedded in the propeptide and also remains in the mature capsid. The phiKZ-like IP proteins are not discernibly homologous to the T4 IP proteins, and it is not known if the phiKZ-like IP proteins are injected into the host cell, or have some other function within the head.
Probab=48.96 E-value=92 Score=23.77 Aligned_cols=52 Identities=25% Similarity=0.321 Sum_probs=42.1
Q ss_pred HhhhHHH--HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 14 QQDWANR--EYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYL 65 (72)
Q Consensus 14 q~DW~nR--e~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~L 65 (72)
.+||..+ +..+.+=.+|+++.+.|..+...--+-...+.+|++.|.+++.-+
T Consensus 52 ~Edlk~~~k~~~~k~~e~i~kl~~~l~~~~~~~~~~~~~~~~r~~~L~~~~~~l 105 (339)
T PF12699_consen 52 LEDLKERAKEAGKKIKEFIKKLIADLKDYAVKFMSGIERVEERIDKLQERAKKL 105 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhh
Confidence 4566553 566677788888999999998888888999999999999888766
No 87
>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Probab=48.94 E-value=34 Score=22.84 Aligned_cols=27 Identities=37% Similarity=0.427 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
-..|-+.+++++..||.+++.|+.++.
T Consensus 103 e~~Ke~~~~~~l~~L~~~i~~L~~~~~ 129 (134)
T PF07047_consen 103 EAKKEEELQERLEELEERIEELEEQVE 129 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345678888999999999999988764
No 88
>PF02185 HR1: Hr1 repeat; InterPro: IPR000861 The HR1 repeat was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN) []. The first two of these repeats were later shown to bind the small G protein rho [, ] known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography []. It forms an antiparallel coiled-coil fold termed an ACC finger. This entry includes domains found within rho-associated protein kinases.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1CXZ_B 3O0Z_C 2RMK_B 1URF_A.
Probab=48.25 E-value=41 Score=19.73 Aligned_cols=30 Identities=27% Similarity=0.334 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 40 FDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 40 F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.-..|..+|...+.||..|+.+|.-|.+..
T Consensus 34 ~~~~~~~~l~~s~~kI~~L~~~L~~l~~~~ 63 (70)
T PF02185_consen 34 VLSEAESQLRESNQKIELLREQLEKLQQRS 63 (70)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 456788888888888888888888776554
No 89
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=48.24 E-value=74 Score=20.59 Aligned_cols=28 Identities=18% Similarity=0.181 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..+.++..+++++..|++....|+..+.
T Consensus 83 ~l~~~~~~l~~~i~~L~~~~~~l~~~~~ 110 (127)
T cd01108 83 LALEHIAELERKIAELQAMRRTLQQLAD 110 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666666666666666666553
No 90
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=47.75 E-value=50 Score=20.53 Aligned_cols=26 Identities=31% Similarity=0.498 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
+..|+..++..+..++..+..+.+++
T Consensus 82 l~~r~~~l~~~~~~l~~~~~~~~~~~ 107 (120)
T PF02996_consen 82 LKKRIKELEEQLEKLEKELAELQAQI 107 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555555555555555555544
No 91
>PF07195 FliD_C: Flagellar hook-associated protein 2 C-terminus; InterPro: IPR010809 The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria []. This alignment covers the C-terminal region of the flagellar hook-associated protein 2.; GO: 0007155 cell adhesion, 0009288 bacterial-type flagellum
Probab=47.62 E-value=58 Score=23.18 Aligned_cols=63 Identities=25% Similarity=0.478 Sum_probs=43.4
Q ss_pred HHHHHHHHHhhhHHHHHHHHH-------------HHhHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 6 REAIQKQIQQDWANREYIEII-------------TGSIKKITDFLNSFDMSC----RSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 6 ~~~v~~~iq~DW~nRe~i~~i-------------n~~I~~~~~FLN~F~~sc----~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
.+....++..|++. +-+++ +.+..++-+.|+.+-..- ..+...++.++..++.+++-+|.+
T Consensus 138 ~~kl~~Al~~np~~--V~~lF~~~~~~~~~~~~~~Gi~~~l~~~l~~~~~~~~G~i~~~~~~l~~~~~~~~~~i~~~~~r 215 (239)
T PF07195_consen 138 ETKLDKALAENPDA--VQALFAGDGTKDGTVYSTSGIATRLNDYLDSYTGSSTGSITSRIDSLNSQIKSLDKQIEDLEER 215 (239)
T ss_pred HHHHHHHHhhCHHH--HHHHHccCccccccccccccHHHHHHHHHHHHhCCCCcchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556667777765 33333 336667777777776555 778888888888888888888887
Q ss_pred hc
Q psy648 69 KS 70 (72)
Q Consensus 69 ls 70 (72)
+.
T Consensus 216 l~ 217 (239)
T PF07195_consen 216 LE 217 (239)
T ss_pred HH
Confidence 65
No 92
>PRK00736 hypothetical protein; Provisional
Probab=47.20 E-value=34 Score=20.63 Aligned_cols=19 Identities=32% Similarity=0.426 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy648 46 SRLAVLNEKLTTLERRIEY 64 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~ 64 (72)
.||..|+.||.-.|..++-
T Consensus 5 ~Ri~~LE~klafqe~tie~ 23 (68)
T PRK00736 5 ERLTELEIRVAEQEKTIEE 23 (68)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444333
No 93
>PRK15471 chain length determinant protein WzzB; Provisional
Probab=46.89 E-value=1.3e+02 Score=23.05 Aligned_cols=38 Identities=21% Similarity=0.282 Sum_probs=29.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 20 REYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLE 59 (72)
Q Consensus 20 Re~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE 59 (72)
++||.|+|.-+.+-. .+++...-+.|...+.++++..|
T Consensus 149 ~~YI~fv~~~v~~~l--~~~i~~~i~~~~~~l~~~~~~~~ 186 (325)
T PRK15471 149 AQYIQQVDDQVAKEL--EKDLKDNIALRTKTLQDSLETQE 186 (325)
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH
Confidence 579999998887655 77787777788888777777666
No 94
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=46.73 E-value=36 Score=20.47 Aligned_cols=23 Identities=35% Similarity=0.453 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Q psy648 48 LAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkls 70 (72)
+..|+++|..|+..+.-+|+.+.
T Consensus 23 v~EL~~RIa~L~aEI~R~~~~~~ 45 (59)
T PF06698_consen 23 VEELEERIALLEAEIARLEAAIA 45 (59)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45778888888888888887664
No 95
>PRK04325 hypothetical protein; Provisional
Probab=46.33 E-value=33 Score=20.98 Aligned_cols=21 Identities=29% Similarity=0.309 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy648 45 RSRLAVLNEKLTTLERRIEYL 65 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~L 65 (72)
+.||..|+.|+.-.|..++-|
T Consensus 8 e~Ri~~LE~klAfQE~tIe~L 28 (74)
T PRK04325 8 EDRITELEIQLAFQEDLIDGL 28 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344555555544444444433
No 96
>PF13864 Enkurin: Calmodulin-binding
Probab=46.28 E-value=34 Score=21.48 Aligned_cols=26 Identities=27% Similarity=0.400 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 42 MSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
.+-+.|-+.|+.+|..||..+.+|+.
T Consensus 70 ~~~~~rK~~lE~~L~qlE~dI~~lsr 95 (98)
T PF13864_consen 70 LRKKRRKEELEKELKQLEKDIKKLSR 95 (98)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 35677889999999999999998863
No 97
>COG4064 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G [Coenzyme metabolism]
Probab=46.23 E-value=37 Score=21.63 Aligned_cols=24 Identities=13% Similarity=0.454 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 47 RLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 47 kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
-+..++.||+.+|+++++.-+.+.
T Consensus 16 dfne~~kRLdeieekvef~~~Ev~ 39 (75)
T COG4064 16 DFNEIHKRLDEIEEKVEFVNGEVY 39 (75)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHH
Confidence 356788999999999998776653
No 98
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=45.93 E-value=73 Score=21.57 Aligned_cols=27 Identities=22% Similarity=0.319 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
-.+.-+..|..|++.||..|+-++.+|
T Consensus 32 ~~E~EI~sL~~K~~~lE~eld~~~~~l 58 (143)
T PF12718_consen 32 QKEQEITSLQKKNQQLEEELDKLEEQL 58 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445555555555555555555544
No 99
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=45.87 E-value=61 Score=20.03 Aligned_cols=37 Identities=27% Similarity=0.385 Sum_probs=25.9
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 27 TGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 27 n~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
...+..|..+++..+. ...+.+.++++.||.++.-|.
T Consensus 57 G~~l~eI~~~l~~~~~---~~~~~l~~~~~~l~~~i~~l~ 93 (96)
T cd04788 57 GFSLREIGRALDGPDF---DPLELLRRQLARLEEQLELAT 93 (96)
T ss_pred CCCHHHHHHHHhCCCh---hHHHHHHHHHHHHHHHHHHHH
Confidence 3456777777776543 566778888888888877665
No 100
>PF15205 PLAC9: Placenta-specific protein 9
Probab=45.76 E-value=49 Score=21.01 Aligned_cols=23 Identities=43% Similarity=0.579 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 46 SRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
+||..++ .++|.+++-|||.|.+
T Consensus 25 ~RLdviE---e~veKTVEhLeaEvk~ 47 (74)
T PF15205_consen 25 SRLDVIE---ETVEKTVEHLEAEVKG 47 (74)
T ss_pred HHHHHHH---HHHHHHHHHHHHHHHH
Confidence 3444444 3456778889998864
No 101
>PF06705 SF-assemblin: SF-assemblin/beta giardin
Probab=45.36 E-value=1.1e+02 Score=21.87 Aligned_cols=42 Identities=21% Similarity=0.302 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 29 SIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 29 ~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
+=..+-++.+++...-..|...++..++.|..++.-|+..+.
T Consensus 68 ~e~~i~~~~~~v~~~~~~~~~~~~~~l~~L~~ri~~L~~~i~ 109 (247)
T PF06705_consen 68 FEEQINNMQERVENQISEKQEQLQSRLDSLNDRIEALEEEIQ 109 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455566666677777777777777777777777766553
No 102
>PF04740 LXG: LXG domain of WXG superfamily; InterPro: IPR006829 This group of putative transposases is found in Gram-positive bacteria, mostly Bacillus members and is thought to be a Cytosolic protein. However, we have also found a Bacillus subtilis bacteriophage SPbetac2 homologue (O64023 from SWISSPROT), possibly arising as a result of horizontal transfer. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=45.29 E-value=95 Score=21.03 Aligned_cols=50 Identities=30% Similarity=0.363 Sum_probs=34.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHH-----HHHHH-HHHHHHHHHHHHHHHHHHhhc
Q psy648 21 EYIEIITGSIKKITDFLNSFDMSC-----RSRLA-VLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 21 e~i~~in~~I~~~~~FLN~F~~sc-----~~kLa-~ln~KL~~LE~~L~~LEAkls 70 (72)
.+++-+...+..+-+|.+.++.+- ++.|. .+..+|..+...+..+...+.
T Consensus 68 ~~~~~~~~~l~~~~~~~~~vd~~~~a~i~e~~L~~el~~~l~~~~~~~~~~~~~~~ 123 (204)
T PF04740_consen 68 LLLEEYQEALKFIKDFQSEVDSSSNAIIDEDFLESELKKKLNQLKEQIEDLQDEIN 123 (204)
T ss_pred HHHHHHHHHHHhHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345555555577777777777643 67777 788888888888877776653
No 103
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=45.04 E-value=38 Score=27.59 Aligned_cols=26 Identities=15% Similarity=0.316 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 46 SRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
.++..++.+|..||.++.-||+++.+
T Consensus 563 ~~~~~~e~~i~~le~~~~~l~~~l~~ 588 (638)
T PRK10636 563 KEIARLEKEMEKLNAQLAQAEEKLGD 588 (638)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 35667777788888888777777754
No 104
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=44.50 E-value=81 Score=20.01 Aligned_cols=38 Identities=16% Similarity=0.197 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 31 KKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 31 ~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
.....+|.+-....+.++..+...++.|+..+..+++.
T Consensus 78 ~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~~~ 115 (116)
T cd04769 78 PHLQQALEDKKQEIRAQITELQQLLARLDAFEASLKDA 115 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 34567788888899999999999999999999888764
No 105
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=43.81 E-value=45 Score=21.47 Aligned_cols=22 Identities=41% Similarity=0.437 Sum_probs=9.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q psy648 48 LAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkl 69 (72)
|..||--|+.||.+-+-|.++|
T Consensus 35 LD~Lns~LD~LE~rnD~l~~~L 56 (83)
T PF03670_consen 35 LDQLNSCLDHLEQRNDHLHAQL 56 (83)
T ss_pred HHHHHHHHHHHHHhhhHHHHHH
Confidence 3344444444444444444443
No 106
>PRK14127 cell division protein GpsB; Provisional
Probab=43.79 E-value=95 Score=20.61 Aligned_cols=25 Identities=16% Similarity=0.283 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 46 SRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..+..|.+++..|+.+|.-++++++
T Consensus 44 ~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 44 KEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3667888888888888888888776
No 107
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=43.63 E-value=56 Score=21.75 Aligned_cols=41 Identities=22% Similarity=0.336 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 29 SIKKITDFLNSFD---MSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 29 ~I~~~~~FLN~F~---~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.+..|-++++-+. ..|......+.+|+..+++++.-|++..
T Consensus 59 sl~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 102 (135)
T PRK10227 59 NLEESGELVNLFNDPQRHSADVKRRTLEKVAEIERHIEELQSMR 102 (135)
T ss_pred CHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777777654 3488888889999999999999988764
No 108
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=43.10 E-value=82 Score=19.65 Aligned_cols=39 Identities=15% Similarity=0.221 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 30 IKKITDFLNSFDM-SCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 30 I~~~~~FLN~F~~-sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
+.-+-+|+..+.. ...++++-|+++++.++.++.-|+..
T Consensus 59 l~~i~~~~~~~~~~~~~~~~~ll~~~~~~l~~~i~~L~~~ 98 (99)
T cd04772 59 YRVAQRIMRAVHAGIVASALALVDAAHALLQRYRQQLDQE 98 (99)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3344566666532 34588999999999999999998865
No 109
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=42.97 E-value=59 Score=20.04 Aligned_cols=22 Identities=32% Similarity=0.462 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q psy648 47 RLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 47 kLa~ln~KL~~LE~~L~~LEAk 68 (72)
++..|+++|+.++..+.-++++
T Consensus 71 ~~~~l~~~l~~l~~~~~~~~~~ 92 (104)
T PF13600_consen 71 ELKELEEELEALEDELAALQDE 92 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555555555544444443
No 110
>PF11690 DUF3287: Protein of unknown function (DUF3287); InterPro: IPR021704 This eukaryotic family of proteins has no known function.
Probab=42.73 E-value=31 Score=23.14 Aligned_cols=24 Identities=29% Similarity=0.412 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHH--HHHHHHHHH
Q psy648 44 CRSRLAVLNEKLTTL--ERRIEYLEA 67 (72)
Q Consensus 44 c~~kLa~ln~KL~~L--E~~L~~LEA 67 (72)
-......|-.|++.| ||++..||+
T Consensus 54 ~~~e~r~L~kKi~~l~veRkmr~Les 79 (109)
T PF11690_consen 54 YCDERRKLRKKIQDLRVERKMRALES 79 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 344567888999999 999999986
No 111
>PF04533 Herpes_U44: Herpes virus U44 protein; InterPro: IPR007619 This entry represents proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. The function is not known, and the proteins are named variously as U44, BSRF1, UL71, and M71. The entry also includes BSRF1.
Probab=42.68 E-value=1e+02 Score=22.93 Aligned_cols=37 Identities=27% Similarity=0.397 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHH
Q psy648 29 SIKKITDFLNSFDM-----SCRSRLAVLNEKLTTLERRIEYL 65 (72)
Q Consensus 29 ~I~~~~~FLN~F~~-----sc~~kLa~ln~KL~~LE~~L~~L 65 (72)
--..+.+||++|.. +|+.-...=-.|++++=..|...
T Consensus 73 Q~n~~~~~L~Rf~~~~cp~h~r~~ve~ei~Klk~I~~vi~n~ 114 (210)
T PF04533_consen 73 QCNNITDYLKRFLSAKCPPHCRPAVETEIQKLKRIQEVIWNT 114 (210)
T ss_pred HHHHHHHHHHHhhhccCChhhHHHHHHHHHHHHHHHHHHHHH
Confidence 55678999999998 78887777777777665555544
No 112
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=42.26 E-value=63 Score=18.10 Aligned_cols=26 Identities=23% Similarity=0.303 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
+.+...|+.+++.|+.....|..+++
T Consensus 24 k~~~~~le~~~~~L~~en~~L~~~i~ 49 (54)
T PF07716_consen 24 KQREEELEQEVQELEEENEQLRQEIA 49 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456666666777766666666554
No 113
>PRK10381 LPS O-antigen length regulator; Provisional
Probab=41.73 E-value=1.5e+02 Score=23.06 Aligned_cols=38 Identities=21% Similarity=0.208 Sum_probs=27.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 20 REYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLE 59 (72)
Q Consensus 20 Re~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE 59 (72)
++||.|+|.-+.+-. ++++...-+.|...+.++++..|
T Consensus 189 ~~YI~fv~~~~~~~l--~~~i~~~~~~k~~~~~~~~~~~~ 226 (377)
T PRK10381 189 SGYINYISTIVVKEV--LENIRNKLEIKTQFEKEKLAMDR 226 (377)
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999988776655 77777766777777776666555
No 114
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.67 E-value=94 Score=19.93 Aligned_cols=40 Identities=30% Similarity=0.437 Sum_probs=20.5
Q ss_pred HHhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 27 TGSIKKITDFLNSFD---MSCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 27 n~~I~~~~~FLN~F~---~sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
...+..|-+||...+ .+|......+.++++.++.++.-|+
T Consensus 57 G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T cd04784 57 DMSLDEIRTLLQLQDDPEASCAEVNALIDEHLAHVRARIAELQ 99 (127)
T ss_pred CCCHHHHHHHHHhhhcCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666777775433 1344444555555555555544443
No 115
>PF13015 PRKCSH_1: Glucosidase II beta subunit-like protein
Probab=41.32 E-value=49 Score=22.91 Aligned_cols=27 Identities=26% Similarity=0.353 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
+..|..++.+++.|+.++..+|..+..
T Consensus 2 ~~~~~~~e~~~~~l~~~i~~~~~~l~~ 28 (154)
T PF13015_consen 2 EKEIDEAERKLSDLESKIRELEDDLNK 28 (154)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 356777888888888888888777653
No 116
>PF05531 NPV_P10: Nucleopolyhedrovirus P10 protein; InterPro: IPR008702 This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra [].; GO: 0019028 viral capsid
Probab=41.22 E-value=57 Score=20.58 Aligned_cols=26 Identities=19% Similarity=0.452 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
-|..+..++.|.+.|+++++-|++.+
T Consensus 9 Ir~dIk~vd~KVdaLq~~V~~l~~~~ 34 (75)
T PF05531_consen 9 IRQDIKAVDDKVDALQTQVDDLESNL 34 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 35566666666666666666655543
No 117
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=40.91 E-value=63 Score=20.89 Aligned_cols=41 Identities=22% Similarity=0.346 Sum_probs=30.7
Q ss_pred HhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 28 GSIKKITDFLNSFD-MSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 28 ~~I~~~~~FLN~F~-~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
..+..|-++|...+ ..|....+.+++++..+|.++.-|+..
T Consensus 57 ~sl~eI~~~l~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~ 98 (124)
T TIGR02051 57 FSLEEIGGLLGLVDGTHCREMYELASRKLKSVQAKMADLLRI 98 (124)
T ss_pred CCHHHHHHHHhcccCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566667776554 468888899999999999998887654
No 118
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=40.88 E-value=66 Score=20.12 Aligned_cols=24 Identities=25% Similarity=0.332 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
..++..+++++..|++....|+.-
T Consensus 77 ~~~~~~l~~~i~~l~~~~~~l~~~ 100 (102)
T cd04789 77 LERLSSLAEQIARKQQARDLLAAL 100 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666666666666654
No 119
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=40.67 E-value=54 Score=23.50 Aligned_cols=27 Identities=22% Similarity=0.478 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
-+.+|.+....|+.++.++.+|+-+++
T Consensus 167 ie~~L~~v~~eIe~~~~~~~~l~~~v~ 193 (262)
T PF14257_consen 167 IERELSRVRSEIEQLEGQLKYLDDRVD 193 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 455666777777777777777776654
No 120
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=40.65 E-value=64 Score=20.84 Aligned_cols=31 Identities=10% Similarity=-0.057 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 34 TDFLNSFDMSCRSRLAVLNEKLTTLERRIEY 64 (72)
Q Consensus 34 ~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~ 64 (72)
..+|..=-..-+.+++.|...++.|+..+..
T Consensus 81 ~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~ 111 (127)
T TIGR02044 81 KARTLEKVAEIERKISELQSMRDQLEALAQA 111 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444444557778888888888888776653
No 121
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=40.44 E-value=40 Score=26.04 Aligned_cols=22 Identities=45% Similarity=0.662 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q psy648 46 SRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~LEA 67 (72)
.|+..+++.|+++|+++..++.
T Consensus 273 ~k~~~~~~q~~~~~k~~~~~~~ 294 (406)
T PF02388_consen 273 NKLKELEEQLASLEKRIEEAEE 294 (406)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 3566666666666666666654
No 122
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=40.42 E-value=1.1e+02 Score=20.44 Aligned_cols=23 Identities=17% Similarity=0.431 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LE 66 (72)
|..++..++.++..||.++.-|.
T Consensus 79 ~~~~~~~l~~~i~~Le~~l~~L~ 101 (134)
T cd04779 79 VAQEVQLVCDQIDGLEHRLKQLK 101 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555555555555555443
No 123
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=40.24 E-value=33 Score=23.71 Aligned_cols=26 Identities=31% Similarity=0.317 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 40 FDMSCRSRLAVLNEKLTTLERRIEYL 65 (72)
Q Consensus 40 F~~sc~~kLa~ln~KL~~LE~~L~~L 65 (72)
-....+..|+.|.+||..-|+-|+-|
T Consensus 125 ~~~~~~~eL~qLq~rL~qTE~~m~ki 150 (152)
T PF15361_consen 125 KRKITDYELAQLQERLAQTERAMEKI 150 (152)
T ss_pred cccchHHHHHHHHHHHHHHHHHHHHH
Confidence 34456788999999999999988754
No 124
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=40.21 E-value=1.1e+02 Score=20.62 Aligned_cols=42 Identities=14% Similarity=0.188 Sum_probs=25.4
Q ss_pred hHHHHHHHHHHHH----HHH-------HHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 29 SIKKITDFLNSFD----MSC-------RSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 29 ~I~~~~~FLN~F~----~sc-------~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.+..|.+|++... ..| ..++..+++++..|++....|+..+.
T Consensus 59 sL~eI~~~l~~~~~~~~~~~~~~~~~l~~~~~~l~~ki~~L~~~~~~L~~~~~ 111 (142)
T TIGR01950 59 PLATIGEALAVLPEGRTPTADDWARLSSQWREELDERIDQLNALRDQLDGCIG 111 (142)
T ss_pred CHHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5667777776543 124 34566666666666666666665543
No 125
>PRK00295 hypothetical protein; Provisional
Probab=40.01 E-value=51 Score=19.82 Aligned_cols=13 Identities=15% Similarity=0.281 Sum_probs=5.0
Q ss_pred HHHHHHHHHHHHH
Q psy648 47 RLAVLNEKLTTLE 59 (72)
Q Consensus 47 kLa~ln~KL~~LE 59 (72)
|+..|+.|+.-.|
T Consensus 6 Ri~~LE~kla~qE 18 (68)
T PRK00295 6 RVTELESRQAFQD 18 (68)
T ss_pred HHHHHHHHHHHHH
Confidence 3333333333333
No 126
>KOG1853|consensus
Probab=39.83 E-value=74 Score=25.02 Aligned_cols=39 Identities=33% Similarity=0.397 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 31 KKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 31 ~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..+-+=||.|-.+.++-=+.|+-.|+.+|.+..-||++.
T Consensus 30 ~~~reEl~EFQegSrE~EaelesqL~q~etrnrdl~t~n 68 (333)
T KOG1853|consen 30 LQMREELNEFQEGSREIEAELESQLDQLETRNRDLETRN 68 (333)
T ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356677899999999999999999999999999999875
No 127
>PRK08724 fliD flagellar capping protein; Validated
Probab=39.76 E-value=1.2e+02 Score=26.05 Aligned_cols=62 Identities=29% Similarity=0.481 Sum_probs=37.7
Q ss_pred HHHHHHHHhhhHHHHHHHHH---HHhHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 7 EAIQKQIQQDWANREYIEII---TGSIKKITDFLNSFD----------MSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 7 ~~v~~~iq~DW~nRe~i~~i---n~~I~~~~~FLN~F~----------~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
+...+++++|-+. +-+++ +.+..++-++|+.+- .+-...+.+++.++..||++|+-+|+++.
T Consensus 574 ~KL~~AL~~npd~--V~~LF~g~~GlA~rL~~~L~~~~~t~G~I~~R~~sL~~~i~~l~dqi~~Le~Rle~~E~Ry~ 648 (673)
T PRK08724 574 DMLDRQLNNNFNK--LEEFFGGNTGFAKRVEDAIQSMTGVTGSIRTREKSLREQNYRLNDDQVALDRRMESLEKRTH 648 (673)
T ss_pred HHHHHHHHhCHHH--HHHHhcCCchHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566665432 22222 456666666666553 34455667777788888888888887764
No 128
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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, an
Probab=39.40 E-value=78 Score=20.21 Aligned_cols=28 Identities=18% Similarity=0.242 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.-..+++.+++++..|++....|+.++.
T Consensus 78 ~l~~~~~~l~~~i~~l~~~~~~L~~~~~ 105 (120)
T cd04781 78 LLKAKAAELDQQIQRLQAMRELLRHVAQ 105 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4456888888888888888888877653
No 129
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=39.36 E-value=93 Score=19.22 Aligned_cols=38 Identities=24% Similarity=0.374 Sum_probs=27.3
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 28 GSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 28 ~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
..|..|-++++.. ++......+..+++.|+.++.-|+.
T Consensus 58 ~~l~eI~~~l~~~--~~~~~~~~l~~~~~~l~~~i~~l~~ 95 (97)
T cd04782 58 ISLKEIKDYLDNR--NPDELIELLKKQEKEIKEEIEELQK 95 (97)
T ss_pred CCHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4566777777653 4567777888888888888887764
No 130
>PF11841 DUF3361: Domain of unknown function (DUF3361)
Probab=39.21 E-value=42 Score=23.71 Aligned_cols=35 Identities=29% Similarity=0.371 Sum_probs=24.4
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 26 ITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 26 in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
-+.||+|++.|+|. ... ....+.++|.+||.=|.+
T Consensus 56 ~~~FI~Kia~~Vn~-~~~----------d~~i~q~sLaILEs~Vl~ 90 (160)
T PF11841_consen 56 SDSFIKKIASYVNS-SAM----------DASILQRSLAILESIVLN 90 (160)
T ss_pred cHHHHHHHHHHHcc-ccc----------cchHHHHHHHHHHHHHhC
Confidence 36799999999992 111 234566889999877654
No 131
>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....
Probab=38.80 E-value=1.4e+02 Score=21.27 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..+.+....+.+...||+.++-||..|
T Consensus 187 eaE~Rae~aE~~v~~Le~~id~le~eL 213 (237)
T PF00261_consen 187 EAENRAEFAERRVKKLEKEIDRLEDEL 213 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555555555544
No 132
>PRK11638 lipopolysaccharide biosynthesis protein WzzE; Provisional
Probab=38.79 E-value=1.8e+02 Score=22.41 Aligned_cols=38 Identities=11% Similarity=0.196 Sum_probs=28.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 20 REYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLE 59 (72)
Q Consensus 20 Re~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE 59 (72)
++||.|+|.-+.+-. .+++...-+.|...+.++++..|
T Consensus 170 ~~YI~fv~~~~~~~l--~~~i~~~~~~~~~~l~~~~~~~~ 207 (342)
T PRK11638 170 RQYVAFASQRAASHL--NDELKGAWAARTIQMKAQVKRQE 207 (342)
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHH
Confidence 578899888877654 77777777777777777766665
No 133
>COG5019 CDC3 Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]
Probab=37.85 E-value=2.1e+02 Score=22.95 Aligned_cols=54 Identities=24% Similarity=0.329 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 18 ANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 18 ~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
.+|++=...+.-|+---+.|-.++.--..++..+|++|.....+++-+|.++.+
T Consensus 314 ~~~~~k~~~~~ki~~~e~~l~~~E~~l~~e~~~~n~~Le~~~~~l~~~e~~l~~ 367 (373)
T COG5019 314 EERELKKKFTEKIREKEKRLEELEQNLIEERKELNSKLEEIQKKLEDLEKRLEK 367 (373)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455555666667777778888888888999999999999999999999998865
No 134
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=37.84 E-value=1.1e+02 Score=19.72 Aligned_cols=42 Identities=26% Similarity=0.349 Sum_probs=31.5
Q ss_pred HhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 28 GSIKKITDFLNSFD---MSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 28 ~~I~~~~~FLN~F~---~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..+..|-+++.... .+|....+.++.++..++.++.-|+...
T Consensus 58 ~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~ 102 (127)
T cd01108 58 FSLEEIRELLALWRDPSRASADVKALALEHIAELERKIAELQAMR 102 (127)
T ss_pred CCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566777776554 4578888899999999999998887643
No 135
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=37.55 E-value=1.9e+02 Score=22.34 Aligned_cols=27 Identities=41% Similarity=0.530 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.|...+..+++++..++..++-|++++
T Consensus 239 ~~~~~~~~l~~~~~~~~~~i~~l~~~l 265 (406)
T PF02388_consen 239 NGKEYLESLQEKLEKLEKEIEKLEEKL 265 (406)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555665555555555555543
No 136
>PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional
Probab=37.19 E-value=64 Score=20.61 Aligned_cols=22 Identities=18% Similarity=0.495 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q psy648 48 LAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkl 69 (72)
+..+..||+.+|.++++-=+.+
T Consensus 17 ~~~i~~rLD~iEeKVEftn~Ei 38 (77)
T PRK01026 17 FKEIQKRLDEIEEKVEFTNAEI 38 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5678889999999998876654
No 137
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=36.81 E-value=1.1e+02 Score=22.39 Aligned_cols=36 Identities=19% Similarity=0.364 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 35 DFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 35 ~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.|.+.|..-+.==|+.++.++..||.+++-|-.+..
T Consensus 94 ~FI~sf~~Y~~leL~s~~~ei~~L~~kI~~L~~~in 129 (181)
T PF04645_consen 94 SFIDSFNQYKNLELKSIKKEIEILRLKISSLQKEIN 129 (181)
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHhh
Confidence 677777777777777777777777777777665544
No 138
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription 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 conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=36.79 E-value=1.1e+02 Score=19.42 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=34.0
Q ss_pred HHhHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 27 TGSIKKITDFLNSFDM----SCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 27 n~~I~~~~~FLN~F~~----sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
...+..|.++|+.++. .|......+..+|+.....|..+..++.
T Consensus 57 G~~l~~I~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~L~~l~~~L~ 104 (107)
T cd01111 57 GIGLDELARLCRALDAGDGKQPEACLAQLRQKIEVRRAALNALTTQLA 104 (107)
T ss_pred CCCHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777888877643 5888888899888888888888888775
No 139
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=36.77 E-value=1.1e+02 Score=19.30 Aligned_cols=42 Identities=12% Similarity=0.128 Sum_probs=26.6
Q ss_pred HhHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 28 GSIKKITDFLNSFD--MSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 28 ~~I~~~~~FLN~F~--~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..+..|.++|+..+ ..|....+.++++++.|+.++.-+...+
T Consensus 58 ~~l~~I~~~l~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~ 101 (108)
T cd04773 58 YLLEQIATVVEQLRHAGGTEALAAALEQRRVALTQRGRAMLDAA 101 (108)
T ss_pred CCHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566777776653 2366666777777777777776665544
No 140
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=36.63 E-value=84 Score=17.94 Aligned_cols=28 Identities=18% Similarity=0.272 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..+..++.++.++..+....+-|+.++.
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~ 48 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIE 48 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666666666666666666666553
No 141
>KOG1760|consensus
Probab=36.46 E-value=1.5e+02 Score=20.71 Aligned_cols=44 Identities=18% Similarity=0.298 Sum_probs=29.2
Q ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 25 IITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 25 ~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
||.+..-++-+-|-.=..+.+..++.|+.++..++++|.-|-+-
T Consensus 74 F~~~~~~~~~~~LEe~ke~l~k~i~~les~~e~I~~~m~~LK~~ 117 (131)
T KOG1760|consen 74 FIHVKLDKLQDQLEEKKETLEKEIEELESELESISARMDELKKV 117 (131)
T ss_pred heeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555566666666666667777777777777777777665543
No 142
>PF12152 eIF_4G1: Eukaryotic translation initiation factor 4G1; InterPro: IPR022745 The eukaryotic initiation factor 4G (eIF4G) is the core of a multicomponent switch controlling gene expression at the level of translation initiation. It interacts with the small ribosomal subunit interacting protein, eIF3, and the eIF4E/cap-mRNA complex in order to load the ribosome onto mRNA during cap-dependent translation. This entry represents the eIF4E-binding domain of eIF4G []. Binding of this domain to its substrate triggers a coupled folding transition where it forms a right-handed helical ring that wraps around the N terminus of eIF4E.; PDB: 1RF8_B.
Probab=36.46 E-value=26 Score=22.00 Aligned_cols=15 Identities=27% Similarity=0.432 Sum_probs=10.2
Q ss_pred HHHHHHHHHHHHHHH
Q psy648 34 TDFLNSFDMSCRSRL 48 (72)
Q Consensus 34 ~~FLN~F~~sc~~kL 48 (72)
.+||-+|...|..|-
T Consensus 58 ~~FLLQF~~v~~~kp 72 (75)
T PF12152_consen 58 PDFLLQFQDVFKEKP 72 (75)
T ss_dssp HHHHHHHHHHH----
T ss_pred HHHHHHHHHHhccCC
Confidence 589999999998874
No 143
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.33 E-value=82 Score=20.23 Aligned_cols=36 Identities=11% Similarity=0.112 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 32 KITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 32 ~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
....+|..=-..-+.+++.|+.....|+..+..+++
T Consensus 77 ~~~~~l~~~~~~l~~~i~~L~~~~~~l~~~~~~~~~ 112 (126)
T cd04783 77 EARELAEQKLAEVDEKIADLQRMRASLQELVSQCAA 112 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 344455444456677888888877877777765554
No 144
>TIGR01149 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G. coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=35.50 E-value=72 Score=20.07 Aligned_cols=22 Identities=14% Similarity=0.462 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q psy648 48 LAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkl 69 (72)
...+..||+.+|.++++-=+.+
T Consensus 14 ~~~i~~rLd~iEeKVEf~~~E~ 35 (70)
T TIGR01149 14 FNEVMKRLDEIEEKVEFVNGEV 35 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4677888999999988876654
No 145
>PF03520 KCNQ_channel: KCNQ voltage-gated potassium channel; InterPro: IPR013821 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. KCNQ channels (also known as KQT-like channels) differ from other voltage-gated 6 TM helix channels, chiefly in that they possess no tetramerisation domain. Consequently, they rely on interaction with accessory subunits, or form heterotetramers with other members of the family []. Currently, 5 members of the KCNQ family are known. These have been found to be widely distributed within the body, having been shown to be expressed in the heart, brain, pancreas, lung, placenta and ear. They were initially cloned as a result of a search for proteins involved in cardiac arhythmia. Subsequently, mutations in other KCNQ family members have been shown to be responsible for some forms of hereditary deafness [] and benign familial neonatal epilepsy []. This entry represents a region found at the C terminus of these proteins.; PDB: 3HFE_B 3HFC_C 3BJ4_B 2OVC_A.
Probab=35.41 E-value=57 Score=24.18 Aligned_cols=25 Identities=16% Similarity=0.549 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 42 MSCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
.+.-+||..++.+++.+|++|+.|-
T Consensus 152 ~sm~~Rl~kvE~qV~~md~KLD~l~ 176 (202)
T PF03520_consen 152 ISMMGRLVKVERQVQSMDKKLDFLV 176 (202)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CchhhHHHHHHHHHHHHHHHHHHHH
Confidence 4556788888888888888888764
No 146
>PF04521 Viral_P18: ssRNA positive strand viral 18kD cysteine rich protein; InterPro: IPR007609 This family represents the 18kDa cysteine-rich protein from ssRNA positive strand viruses.
Probab=35.28 E-value=60 Score=22.29 Aligned_cols=22 Identities=45% Similarity=0.513 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q psy648 48 LAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkl 69 (72)
|.++|.+|+.||++-+.|=+++
T Consensus 74 l~~~~~~L~~Le~r~e~Lk~~~ 95 (120)
T PF04521_consen 74 LSDLNLELEKLERREEQLKTQI 95 (120)
T ss_pred hhhHHHHHHHHHHHHHHHHHHH
Confidence 6778888888888888776643
No 147
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=35.03 E-value=1.3e+02 Score=19.44 Aligned_cols=34 Identities=12% Similarity=0.067 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 36 FLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 36 FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.|.+=-..-+.+++.++..++.|+..+...++++
T Consensus 84 ~l~~~~~~l~~~~~~l~~~~~~L~~~~~~~~~~~ 117 (118)
T cd04776 84 KIEKRRAELEQQRRDIDAALAELDAAEERCRERL 117 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3333333444455555555555555555555544
No 148
>PRK13723 conjugal transfer pilus assembly protein TraH; Provisional
Probab=34.79 E-value=2.2e+02 Score=23.20 Aligned_cols=48 Identities=10% Similarity=0.344 Sum_probs=38.3
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 20 REYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 20 Re~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
.+.+.-+...|...-+|+..+......| ...++.+++.+.++|.+|++
T Consensus 390 ~~~~~~~~~~l~~a~~~~~~~~~~~~~~----~~~~~~i~~~~~~~eqq~~~ 437 (451)
T PRK13723 390 EAVMDHLRENLNQAQRQIAAFQSQVQVQ----QDALLVVDRQMSYMRQQLSA 437 (451)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH
Confidence 5566777788888888899888888777 44567889999999988875
No 149
>PF13870 DUF4201: Domain of unknown function (DUF4201)
Probab=34.64 E-value=90 Score=21.18 Aligned_cols=38 Identities=26% Similarity=0.538 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 32 KITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 32 ~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
....-+-.|+ .|...+..+...+..+++++.++|-+++
T Consensus 139 ~~P~ll~Dy~-~~~~~~~~l~~~i~~l~rk~~~l~~~i~ 176 (177)
T PF13870_consen 139 GVPALLRDYD-KTKEEVEELRKEIKELERKVEILEMRIK 176 (177)
T ss_pred CCcHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4455566676 7888999999999999999999998875
No 150
>PF14916 CCDC92: Coiled-coil domain of unknown function
Probab=34.47 E-value=42 Score=20.36 Aligned_cols=19 Identities=26% Similarity=0.602 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q psy648 51 LNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 51 ln~KL~~LE~~L~~LEAkl 69 (72)
|+.+++.+|++|.||..+-
T Consensus 1 l~~qv~s~e~~i~FLq~eH 19 (60)
T PF14916_consen 1 LEQQVQSLEKSILFLQQEH 19 (60)
T ss_pred ChHHHHHHHHHHHHHHHHH
Confidence 4678999999999997653
No 151
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=34.31 E-value=53 Score=18.49 Aligned_cols=17 Identities=29% Similarity=0.587 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy648 42 MSCRSRLAVLNEKLTTL 58 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~L 58 (72)
..|+.+|...+.+++.|
T Consensus 37 ~~c~~~L~~~e~~i~~l 53 (53)
T PF02609_consen 37 KKCQERLEEAEQKIEEL 53 (53)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhC
Confidence 46777777777776654
No 152
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=34.19 E-value=1.1e+02 Score=18.63 Aligned_cols=28 Identities=25% Similarity=0.341 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.++++++.|.+|...||..=.+|-...+
T Consensus 18 vLK~~I~eL~~~n~~Le~EN~~Lk~~~~ 45 (59)
T PF01166_consen 18 VLKEQIAELEERNSQLEEENNLLKQNAS 45 (59)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 5688999999999999988877765543
No 153
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=34.18 E-value=1.4e+02 Score=19.60 Aligned_cols=33 Identities=30% Similarity=0.459 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHhhc
Q psy648 38 NSFDMSCRSRLAVLN----EKLTTLERRIEYLEARKS 70 (72)
Q Consensus 38 N~F~~sc~~kLa~ln----~KL~~LE~~L~~LEAkls 70 (72)
..|+.....-|..|+ +.++.|+.+|+-||++|.
T Consensus 77 ~~~~~~v~~~L~~lg~~tk~ev~~L~~RI~~Le~~l~ 113 (118)
T TIGR01837 77 KAFDERVEQALNRLNIPSREEIEALSAKIEQLAVQVE 113 (118)
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 355666666666666 778999999999999885
No 154
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=34.14 E-value=92 Score=20.23 Aligned_cols=28 Identities=14% Similarity=0.209 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.-+.++..++.++..|+.....|+..+.
T Consensus 83 ~l~~~~~~l~~~i~~L~~~~~~L~~~~~ 110 (127)
T TIGR02047 83 LLDEHISHVRARIIKLQALIEQLVDLRG 110 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4467888888888888888888876543
No 155
>PF04912 Dynamitin: Dynamitin ; InterPro: IPR006996 Dynamitin is a subunit of the microtubule-dependent motor complex, it is also implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS) []. It is also thought to modulate cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organisation during mitosis. Dynamitin is also involved in anchoring microtubules to centrosomes and may play a role in synapse formation during brain development []. ; GO: 0007017 microtubule-based process, 0005869 dynactin complex
Probab=33.86 E-value=43 Score=25.68 Aligned_cols=21 Identities=29% Similarity=0.332 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy648 44 CRSRLAVLNEKLTTLERRIEY 64 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~ 64 (72)
--.|++.|+.||..||+.|..
T Consensus 207 ~la~~a~LE~RL~~LE~~lG~ 227 (388)
T PF04912_consen 207 QLARAADLEKRLARLESALGI 227 (388)
T ss_pred HHHHHHHHHHHHHHHHHHhCC
Confidence 456777777777777766654
No 156
>PRK00846 hypothetical protein; Provisional
Probab=33.73 E-value=67 Score=20.19 Aligned_cols=16 Identities=38% Similarity=0.702 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHHHH
Q psy648 51 LNEKLTTLERRIEYLE 66 (72)
Q Consensus 51 ln~KL~~LE~~L~~LE 66 (72)
++.||..||.++.+.|
T Consensus 11 le~Ri~~LE~rlAfQe 26 (77)
T PRK00846 11 LEARLVELETRLSFQE 26 (77)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444444443
No 157
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=33.58 E-value=1.2e+02 Score=18.84 Aligned_cols=35 Identities=20% Similarity=0.322 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 34 TDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 34 ~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
.+||.+=-...+..+..++..+..+...+.-+++.
T Consensus 89 ~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~ 123 (129)
T cd00890 89 IEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEE 123 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444333344444444444444444444444443
No 158
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=33.48 E-value=71 Score=20.53 Aligned_cols=31 Identities=32% Similarity=0.516 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 36 FLNSFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 36 FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
|.--|..+ -|+..+++|+.+|=+.+.++|+.
T Consensus 78 l~~~~~l~--~~is~le~~i~~L~qeiAl~e~~ 108 (115)
T PF10066_consen 78 LVIIFSLY--VRISRLEEKIKRLAQEIALLEAE 108 (115)
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHHHHhhh
Confidence 33444444 47889999999999999999875
No 159
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=33.09 E-value=1.5e+02 Score=19.67 Aligned_cols=32 Identities=16% Similarity=0.178 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 38 NSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 38 N~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
......-+.|+..+++++..|++....|+..+
T Consensus 80 ~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~ 111 (140)
T PRK09514 80 QEVKGIVDEKLAEVEAKIAELQHMRRSLQRLN 111 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44556678888899999888888777777654
No 160
>PF14586 MHC_I_2: Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2; PDB: 1JFM_E.
Probab=33.06 E-value=61 Score=23.40 Aligned_cols=38 Identities=18% Similarity=0.473 Sum_probs=27.8
Q ss_pred HHHHHhhhHH-HHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q psy648 10 QKQIQQDWAN-REYIEIITGSIKKITDFLNSFDMSCRSR 47 (72)
Q Consensus 10 ~~~iq~DW~n-Re~i~~in~~I~~~~~FLN~F~~sc~~k 47 (72)
-..|.+-|++ |++..++..+|..--..|+.|=..+++|
T Consensus 136 a~~i~e~We~d~~L~~~l~~~~gDc~~wl~eFL~~~kE~ 174 (174)
T PF14586_consen 136 ARGIKEEWENDRDLAQHLKFSMGDCSHWLKEFLKHSKEK 174 (174)
T ss_dssp HHHHHHHHHTBHHHHHHHHHHHHHHHHHHHHHHHCTS--
T ss_pred hhhHHHHhhccHHHHHHHHHHhcccHHHHHHHHHhhccC
Confidence 3568889986 5555588888888888888888777765
No 161
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=32.93 E-value=78 Score=21.66 Aligned_cols=25 Identities=40% Similarity=0.469 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 47 RLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 47 kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
|=+.++.|++++|..|+-+....++
T Consensus 67 kwaKl~Rk~~kl~~el~~~~~~~~~ 91 (161)
T PF04420_consen 67 KWAKLNRKLDKLEEELEKLNKSLSS 91 (161)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556778888888887777666543
No 162
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=32.22 E-value=68 Score=25.92 Aligned_cols=39 Identities=23% Similarity=0.206 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHh
Q psy648 30 IKKITDFLNSFDMSCRSRLAVLNEKLTTLER---RIEYLEAR 68 (72)
Q Consensus 30 I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~---~L~~LEAk 68 (72)
|+-=-.|+|..-.--++|++.|++||+.+|- ..+.+||-
T Consensus 77 ikfD~~~~n~l~kkneeki~Elde~i~~~eedngE~e~~ea~ 118 (412)
T COG5187 77 IKFDRGRMNTLLKKNEEKIEELDERIREKEEDNGETEGSEAD 118 (412)
T ss_pred eehhhHHHHHHHHhhHHHHHHHHHHHHHHhhcccchHHHHHH
Confidence 4444567787777889999999999999885 44556654
No 163
>PF15003 HAUS2: HAUS augmin-like complex subunit 2
Probab=32.06 E-value=2.4e+02 Score=21.82 Aligned_cols=27 Identities=7% Similarity=0.272 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHH
Q psy648 19 NREYIEIITGSIKKITDFLNSFDMSCR 45 (72)
Q Consensus 19 nRe~i~~in~~I~~~~~FLN~F~~sc~ 45 (72)
+++|=.++-+.+..++.|+.++..+|+
T Consensus 128 EA~yHr~vVeLL~laa~fi~~Le~~Le 154 (277)
T PF15003_consen 128 EAQYHRYVVELLELAASFIEKLEEHLE 154 (277)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677788899999999999999998
No 164
>PF03954 Lectin_N: Hepatic lectin, N-terminal domain; InterPro: IPR005640 Animal lectins display a wide variety of architectures. They are classified according to the carbohydrate-recognition domain (CRD) of which there are two main types, S-type and C-type. C-type lectins display a wide range of specificities. They require Ca2+ for their activity They are found predominantly but not exclusively in vertebrates. This entry presents N-terminal domain, which is found in C-type lectins.; GO: 0005529 sugar binding, 0016020 membrane
Probab=32.03 E-value=33 Score=24.01 Aligned_cols=33 Identities=21% Similarity=0.355 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 37 LNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 37 LN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
+++|.++++.-+-.|+-.=..+.+++--|||++
T Consensus 71 fsNFssst~aEvqaL~S~G~sl~~kVtSLea~l 103 (138)
T PF03954_consen 71 FSNFSSSTLAEVQALSSQGGSLQDKVTSLEAKL 103 (138)
T ss_pred HhcccHHHHHHHHHHHhccccHHhHcccHHHHH
Confidence 567777777776666544444444444444444
No 165
>PRK06798 fliD flagellar capping protein; Validated
Probab=31.60 E-value=94 Score=24.68 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=24.7
Q ss_pred HHhHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 27 TGSIKKITDFLNSFD----------MSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 27 n~~I~~~~~FLN~F~----------~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
+.+..++-+.|+.+- .+-+.++..++.++..+|++++-.|.++
T Consensus 357 ~Gia~~l~~~l~~~~~~~G~i~~r~~~l~~~i~~l~~~~~~~e~rl~~~e~~l 409 (440)
T PRK06798 357 NGLGKEMEKSLDKIFGDEGIIGERSKSIDNRVSKLDLKITDIDTQNKQKQDNI 409 (440)
T ss_pred CcHHHHHHHHHHhhhCCCceeehhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445556666665554 2345556666666666666666655554
No 166
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=31.39 E-value=1.3e+02 Score=18.63 Aligned_cols=42 Identities=21% Similarity=0.177 Sum_probs=28.2
Q ss_pred HhHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 28 GSIKKITDFLNSFDM-------SCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 28 ~~I~~~~~FLN~F~~-------sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..+..|-+|+..... .|....+-+..|+..+|.++.-|...+
T Consensus 56 ~sL~eI~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~ 104 (107)
T cd04777 56 FSLIEIQKIFSYKRLTKSRTHEDQDYYKSFLKNKKDELEKEIEDLKKAI 104 (107)
T ss_pred CCHHHHHHHHHhcccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456777777765421 245556778888888888887776654
No 167
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=31.29 E-value=87 Score=22.11 Aligned_cols=26 Identities=19% Similarity=0.356 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
-+..++.+.++|..||+.+..+-.+|
T Consensus 90 Le~~~~~l~~ri~eLe~~l~~kad~v 115 (175)
T PRK13182 90 LEAQLNTITRRLDELERQLQQKADDV 115 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 45555556666666666555554444
No 168
>cd03182 GST_C_GTT2_like GST_C family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. GTT2, a homodimer, exhibits GST activity with standard substrates. Strains with deleted GTT2 genes are viable but exhibit increased sensiti
Probab=31.27 E-value=99 Score=18.34 Aligned_cols=22 Identities=14% Similarity=0.126 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhcc
Q psy648 50 VLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 50 ~ln~KL~~LE~~L~~LEAklss 71 (72)
..++-.+++++.+.+||+.|+.
T Consensus 46 ~~~~~~~~l~~~l~~le~~L~~ 67 (117)
T cd03182 46 WGERSKARAADFLAYLDTRLAG 67 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHhcC
Confidence 4566778899999999998853
No 169
>PF13220 DUF4028: Protein of unknown function (DUF4028)
Probab=30.97 E-value=33 Score=21.12 Aligned_cols=12 Identities=50% Similarity=1.088 Sum_probs=9.0
Q ss_pred HHHHHhhhH-HHH
Q psy648 10 QKQIQQDWA-NRE 21 (72)
Q Consensus 10 ~~~iq~DW~-nRe 21 (72)
-+.+..||. |||
T Consensus 44 fkevekdwkenre 56 (65)
T PF13220_consen 44 FKEVEKDWKENRE 56 (65)
T ss_pred HHHHHHHHHHhhh
Confidence 467899994 676
No 170
>PF14435 SUKH-4: SUKH-4 immunity protein
Probab=30.93 E-value=87 Score=20.83 Aligned_cols=46 Identities=24% Similarity=0.277 Sum_probs=28.7
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHhh
Q psy648 23 IEIITGSIKKITDFLNSFDMSCRSRLAVLNE---KLTTLERRIEYLEARK 69 (72)
Q Consensus 23 i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~---KL~~LE~~L~~LEAkl 69 (72)
..+||..|-+.+.||..|..-.+ ++...+. --...|+-.+-|..++
T Consensus 109 ~~~vNssl~~f~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~l 157 (179)
T PF14435_consen 109 PVFVNSSLSSFARCLALFERMIR-ELAELNDEDIDFDEPEALAERLREEL 157 (179)
T ss_pred ceeccCCHHHHHHHHHHHHHHHH-HHhhccccccchhhHHHHHHHHHHHH
Confidence 56899999999999999985444 4444443 1344444444444443
No 171
>PF07439 DUF1515: Protein of unknown function (DUF1515); InterPro: IPR010889 This family consists of several hypothetical bacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Rhizobium species. The function of this family is unknown.
Probab=30.85 E-value=1.2e+02 Score=20.62 Aligned_cols=29 Identities=41% Similarity=0.460 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
+.-.|+..|-+++..||.++.-|.+.++.
T Consensus 37 ~mhrRlDElV~Rv~~lEs~~~~lk~dVse 65 (112)
T PF07439_consen 37 SMHRRLDELVERVTTLESSVSTLKADVSE 65 (112)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHhhHHh
Confidence 34568889999999999999999888763
No 172
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=30.60 E-value=2.3e+02 Score=22.40 Aligned_cols=25 Identities=12% Similarity=0.193 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
...+..++.++..++.++.-|+.++
T Consensus 144 ~~~~~~~~~~~~~~~~~l~~l~~~l 168 (525)
T TIGR02231 144 LTEDREAERRIRELEKQLSELQNEL 168 (525)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555666666665554
No 173
>cd03184 GST_C_Omega GST_C family, Class Omega subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Class Omega GSTs show little or no GSH-conjugating activity towards standard GST substrates. Instead, they catalyze the GSH dependent reduction of protein disulfides, dehydroascorbate and monomethylarsonate, activities which are more characteristic of glutaredoxins. They contain a conserved cysteine equivalent to the first cysteine in the CXXC motif of glutaredoxins, which is a re
Probab=30.56 E-value=1.3e+02 Score=18.44 Aligned_cols=46 Identities=20% Similarity=0.215 Sum_probs=29.0
Q ss_pred hHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 17 WANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 17 W~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
+.+|=++++++..+.....++-. .. ......+.+.+.+..||..++
T Consensus 4 a~~r~~~~~~~~~~~~~~~~~~~-----~~---~~~~~~~~~~~~l~~le~~L~ 49 (124)
T cd03184 4 AQQKLLLERFSKVVSAFYKLLGA-----PS---DREEKKAELRSALENLEEELT 49 (124)
T ss_pred HHHHHHHHHHhhhhHHHHHHHhc-----cc---cchhhHHHHHHHHHHHHHHHH
Confidence 45677777887666666655543 22 233455677777777777775
No 174
>PF13805 Pil1: Eisosome component PIL1; PDB: 3PLT_B.
Probab=30.48 E-value=67 Score=24.56 Aligned_cols=26 Identities=31% Similarity=0.308 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
..||..|++.|...|.....-||+|+
T Consensus 164 s~kl~~LeqELvraEae~lvaEAqL~ 189 (271)
T PF13805_consen 164 SPKLVVLEQELVRAEAENLVAEAQLS 189 (271)
T ss_dssp TTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 35888899999999998888888875
No 175
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=30.33 E-value=90 Score=19.38 Aligned_cols=24 Identities=33% Similarity=0.480 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 48 LAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAklss 71 (72)
.+.|++||-.|-..++-|+|++.+
T Consensus 27 V~El~eRIalLq~EIeRlkAe~~k 50 (65)
T COG5509 27 VAELEERIALLQAEIERLKAELAK 50 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356788888888888888887653
No 176
>TIGR01280 xseB exodeoxyribonuclease VII, small subunit. This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides.
Probab=30.21 E-value=67 Score=19.29 Aligned_cols=19 Identities=21% Similarity=0.429 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy648 41 DMSCRSRLAVLNEKLTTLE 59 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~LE 59 (72)
...|+.+|...+.|++.|-
T Consensus 38 ~k~c~~~L~~ae~kv~~l~ 56 (67)
T TIGR01280 38 ARRCEKKLAQAEQRVRKLL 56 (67)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3578888888888877764
No 177
>PF02370 M: M protein repeat; InterPro: IPR003345 This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis [].; PDB: 2KK9_A.
Probab=29.96 E-value=80 Score=15.62 Aligned_cols=16 Identities=25% Similarity=0.239 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHH
Q psy648 51 LNEKLTTLERRIEYLE 66 (72)
Q Consensus 51 ln~KL~~LE~~L~~LE 66 (72)
|+-++++||....++|
T Consensus 6 lEa~~qkLe~e~q~~e 21 (21)
T PF02370_consen 6 LEADHQKLEAEKQISE 21 (21)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhcC
Confidence 4555555555555443
No 178
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=29.84 E-value=1.5e+02 Score=18.78 Aligned_cols=27 Identities=15% Similarity=0.271 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.|+.++..++.++..++.++.-++.++
T Consensus 78 ~ie~~i~~lek~~~~l~~~l~e~q~~l 104 (110)
T TIGR02338 78 TLELRVKTLQRQEERLREQLKELQEKI 104 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346666666666666666666666554
No 179
>PF08393 DHC_N2: Dynein heavy chain, N-terminal region 2; InterPro: IPR013602 Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. Dyneins generally contain one to three heavy chains, where each heavy chain consists of a C-terminal globular head, a flexible microtubule-binding stalk, and a flexible N-terminal tail known as the cargo-binding domain []. The two categories of dyneins are the axonemal dyneins, which produce the bending motions that propagate along cilia and flagella, and the cytosolic dyneins, which drive a variety of fundamental cellular processes including nuclear migration, organisation of the mitotic spindle, chromosome separation during mitosis, and the positioning and function of many intracellular organelles. Cytoplasmic dyneins contain several accessory subunits ranging from light to intermediate chains. This entry represents a region found C-terminal to the dynein heavy chain N-terminal region 1 (IPR013594 from INTERPRO) in many members of this family. No functions seem to have been attributed specifically to this region. ; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.
Probab=29.74 E-value=79 Score=23.64 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHH-HHHHHh
Q psy648 42 MSCRSRLAVLNEKLTTLERRI-EYLEAR 68 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE~~L-~~LEAk 68 (72)
..+.+.|..++..|..+.++| +|||.|
T Consensus 280 ~~~~~~l~~~~~~l~~i~k~L~~~Le~k 307 (408)
T PF08393_consen 280 PDLLEKLESINESLEKIQKSLNDYLESK 307 (408)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHhHHHHHH
Confidence 457899999999999999998 567765
No 180
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=29.56 E-value=1.4e+02 Score=18.37 Aligned_cols=38 Identities=26% Similarity=0.433 Sum_probs=18.1
Q ss_pred hHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 29 SIKKITDFLNSFD----MSCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 29 ~I~~~~~FLN~F~----~sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
.|..+...+..+. ..-..+.+.|++++..|+..+..|+
T Consensus 59 ~l~~i~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~ 100 (103)
T cd01106 59 SLKEIKELLKDPSEDLLEALREQKELLEEKKERLDKLIKTID 100 (103)
T ss_pred CHHHHHHHHHcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555443 3334444455555555555554444
No 181
>PF12125 Beta-TrCP_D: D domain of beta-TrCP; InterPro: IPR021977 This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found associated with PF00646 from PFAM, PF00400 from PFAM. The protein that contains this domain functions as a ubiquitin ligase. Ubiquitination is required to direct proteins towards the proteasome for degradation. This protein is part of the WD40 class of F box proteins. The D domain of these F box proteins is involved in mediating the dimerisation of the protein. Dimerisation is necessary to polyubiquitinate substrates so this D domain is vital in directing substrates towards the proteasome for degradation. ; PDB: 2P64_A 1P22_A.
Probab=29.49 E-value=44 Score=18.99 Aligned_cols=22 Identities=9% Similarity=0.593 Sum_probs=17.3
Q ss_pred hhhHHHHHHHHHHHhHHHHHHH
Q psy648 15 QDWANREYIEIITGSIKKITDF 36 (72)
Q Consensus 15 ~DW~nRe~i~~in~~I~~~~~F 36 (72)
..|...|-+.||-..|.++.-|
T Consensus 5 ~~Wse~eQvdFVe~Ll~rM~H~ 26 (40)
T PF12125_consen 5 DKWSESEQVDFVEQLLSRMCHY 26 (40)
T ss_dssp TTS-HHHHHHHHHHHHHTS-HH
T ss_pred hccCchhHHHHHHHHHHHHHHH
Confidence 4699999999999999888765
No 182
>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=29.15 E-value=1e+02 Score=16.69 Aligned_cols=45 Identities=18% Similarity=0.261 Sum_probs=34.5
Q ss_pred HHHHHHHhhhHHHHHHHHHHHhHHHHHHHHH-HHHHHHHHHHHHHH
Q psy648 8 AIQKQIQQDWANREYIEIITGSIKKITDFLN-SFDMSCRSRLAVLN 52 (72)
Q Consensus 8 ~v~~~iq~DW~nRe~i~~in~~I~~~~~FLN-~F~~sc~~kLa~ln 52 (72)
.+...++..+.+-.....+...+.++.+++. .+...|+.=+..+-
T Consensus 8 ~~v~~~~~~~~~~~~~~~i~~~~~~~C~~~~~~~~~~C~~~v~~~~ 53 (76)
T smart00741 8 DVVKQLENLLKDNKTEEEIKKALEKVCKKLPKSLSDQCKEFVDQYG 53 (76)
T ss_pred HHHHHHHHHHHhchHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHH
Confidence 3455666666666667888899999999999 89999997666543
No 183
>PF10400 Vir_act_alpha_C: Virulence activator alpha C-term; InterPro: IPR018309 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response []. This entry represents the C-terminal domain.; PDB: 1YG2_A.
Probab=28.88 E-value=1.3e+02 Score=17.62 Aligned_cols=27 Identities=19% Similarity=0.169 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 31 KKITDFLNSFDMSCRSRLAVLNEKLTT 57 (72)
Q Consensus 31 ~~~~~FLN~F~~sc~~kLa~ln~KL~~ 57 (72)
..+...|.++...|+.+|+.++...+.
T Consensus 20 ~~~~~~l~~~~~~~~~~l~~~~~~~~~ 46 (90)
T PF10400_consen 20 EEAIELLEERREQHEERLAEYEEIEQE 46 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566677777777777777765544
No 184
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=28.83 E-value=93 Score=25.24 Aligned_cols=24 Identities=38% Similarity=0.436 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 48 LAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAklss 71 (72)
+..++.+|..||.++.-||++++.
T Consensus 570 ~~~~e~~i~~le~~~~~~~~~~~~ 593 (635)
T PRK11147 570 LEQLPQLLEDLEAEIEALQAQVAD 593 (635)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcC
Confidence 666777777777777777766654
No 185
>KOG1029|consensus
Probab=28.26 E-value=3.1e+02 Score=25.00 Aligned_cols=64 Identities=25% Similarity=0.380 Sum_probs=45.9
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHhH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 6 REAIQKQIQQDWANREYIEIITGSI---KKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 6 ~~~v~~~iq~DW~nRe~i~~in~~I---~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
++..-++=|..|+.-..-+..|.-= ..++ .||.=-..-.-.|.+||.|++.|+-+|.-.++.+.
T Consensus 402 r~ElEkqRqlewErar~qem~~Qk~reqe~iv-~~nak~~ql~~eletLn~k~qqls~kl~Dvr~~~t 468 (1118)
T KOG1029|consen 402 REELEKQRQLEWERARRQEMLNQKNREQEWIV-YLNAKKKQLQQELETLNFKLQQLSGKLQDVRVDIT 468 (1118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHhhhhhhheeccc
Confidence 4556677788898776666665432 2222 26666666777899999999999999988877664
No 186
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=28.24 E-value=58 Score=26.88 Aligned_cols=27 Identities=19% Similarity=0.343 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
..||+.|..+|+.|+.++..|..+|++
T Consensus 30 ~qkie~L~kql~~Lk~q~~~l~~~v~k 56 (489)
T PF11853_consen 30 LQKIEALKKQLEELKAQQDDLNDRVDK 56 (489)
T ss_pred HHHHHHHHHHHHHHHHhhcccccccch
Confidence 349999999999999998877766653
No 187
>PHA03385 IX capsid protein IX,hexon associated protein IX; Provisional
Probab=28.12 E-value=1.5e+02 Score=20.81 Aligned_cols=29 Identities=21% Similarity=0.320 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 42 MSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
...+.||..+-.+|..|-++|..|-.||.
T Consensus 96 ~~~ed~L~~llaqLealsqqL~~ls~qv~ 124 (135)
T PHA03385 96 SLAEDKLLVLLAQLEALSQQLQELSQQVA 124 (135)
T ss_pred hhhHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44588999998889888888888877764
No 188
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=27.98 E-value=1.9e+02 Score=19.39 Aligned_cols=39 Identities=28% Similarity=0.457 Sum_probs=18.9
Q ss_pred hHHHHHHHHHHHH-HHHHH-------HHHHHHHHHHHHHHHHHHHHH
Q psy648 29 SIKKITDFLNSFD-MSCRS-------RLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 29 ~I~~~~~FLN~F~-~sc~~-------kLa~ln~KL~~LE~~L~~LEA 67 (72)
.+..|.++|...+ ..|.. |+..+++|++.|++....|..
T Consensus 66 sL~eI~~ll~~~~~~~~~~~~~ll~~k~~~l~~~i~~L~~~~~~L~~ 112 (144)
T PRK13752 66 SLDEIAELLRLEDGTHCEEASSLAEHKLKDVREKMADLARMEAVLSE 112 (144)
T ss_pred CHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666664322 23444 455555555555555444444
No 189
>PRK00965 tetrahydromethanopterin S-methyltransferase subunit B; Provisional
Probab=27.95 E-value=76 Score=20.91 Aligned_cols=23 Identities=22% Similarity=0.320 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Q psy648 48 LAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkls 70 (72)
+.-+++++++||.-.+-||..|+
T Consensus 33 ~~pi~E~i~kLe~~addL~nsLd 55 (96)
T PRK00965 33 MDPIEEEINKLEALADDLENSLD 55 (96)
T ss_pred chHHHHHHHHHHHHHHHHHhccC
Confidence 46688999999999999988765
No 190
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=27.71 E-value=1.4e+02 Score=17.87 Aligned_cols=27 Identities=26% Similarity=0.333 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.++.||-..+.|...|++.|.-|+-++
T Consensus 29 ~~e~kLqeaE~rn~eL~~ei~~L~~e~ 55 (61)
T PF08826_consen 29 AFESKLQEAEKRNRELEQEIERLKKEM 55 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567888888888888888888877655
No 191
>PF12709 Kinetocho_Slk19: Central kinetochore-associated; InterPro: IPR024312 This is a family of proteins integrally involved in the central kinetochore. Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed [].
Probab=27.66 E-value=1.8e+02 Score=18.86 Aligned_cols=50 Identities=14% Similarity=0.180 Sum_probs=37.8
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 22 YIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 22 ~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
++.+=+---.++...=-.++..-+.++..|..++..+.+.++-|.+++..
T Consensus 25 h~~YssKHE~KV~~LKksYe~rwek~v~~L~~e~~~l~~E~e~L~~~l~~ 74 (87)
T PF12709_consen 25 HALYSSKHETKVKALKKSYEARWEKKVDELENENKALKRENEQLKKKLDT 74 (87)
T ss_pred HHHHhhHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444555555556788889999999999999999999999888753
No 192
>PRK14063 exodeoxyribonuclease VII small subunit; Provisional
Probab=27.55 E-value=77 Score=19.55 Aligned_cols=17 Identities=18% Similarity=0.507 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy648 42 MSCRSRLAVLNEKLTTL 58 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~L 58 (72)
..|+.+|...+.|++.|
T Consensus 43 k~C~~~L~~aE~ki~~l 59 (76)
T PRK14063 43 KLCDEKLKNVQEQMAVI 59 (76)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 46888888887777654
No 193
>KOG4603|consensus
Probab=27.53 E-value=1.3e+02 Score=22.26 Aligned_cols=28 Identities=25% Similarity=0.453 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.-..++..|.+|++.|-.+..++||.+.
T Consensus 83 ~ld~~i~~l~ek~q~l~~t~s~veaEik 110 (201)
T KOG4603|consen 83 VLDGKIVALTEKVQSLQQTCSYVEAEIK 110 (201)
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456777778888888888888888764
No 194
>PF13410 GST_C_2: Glutathione S-transferase, C-terminal domain; PDB: 4DEJ_H 3IC8_A 2JL4_A 2V6K_B 3CBU_B 1JLW_B 3F6D_B 3G7I_A 3F63_A 3G7J_B ....
Probab=27.43 E-value=1.1e+02 Score=16.61 Aligned_cols=21 Identities=19% Similarity=0.289 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHhhcc
Q psy648 51 LNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 51 ln~KL~~LE~~L~~LEAklss 71 (72)
.++-.+.+++.++.||..++.
T Consensus 4 ~~~~~~~~~~~l~~le~~L~~ 24 (69)
T PF13410_consen 4 VERARAQLEAALDALEDHLAD 24 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 445567778888888887764
No 195
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=27.34 E-value=1.2e+02 Score=16.75 Aligned_cols=30 Identities=23% Similarity=0.327 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 37 LNSFDMSCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 37 LN~F~~sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
|..+...+......++..++.|+..+..|.
T Consensus 9 l~~~a~~~~~~~~~l~~~~~~l~~~~~~l~ 38 (86)
T PF06013_consen 9 LRAAAQQLQAQADELQSQLQQLESSIDSLQ 38 (86)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344444555555556666666666665553
No 196
>PF13314 DUF4083: Domain of unknown function (DUF4083)
Probab=27.22 E-value=1.1e+02 Score=18.64 Aligned_cols=15 Identities=40% Similarity=0.592 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy648 50 VLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 50 ~ln~KL~~LE~~L~~LEA 67 (72)
.+| |+|+|-++.||.
T Consensus 43 ~~e---qKLDrIIeLLEK 57 (58)
T PF13314_consen 43 SME---QKLDRIIELLEK 57 (58)
T ss_pred HHH---HHHHHHHHHHcc
Confidence 577 455566777774
No 197
>PF12841 YvrJ: YvrJ protein family; InterPro: IPR024419 This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI [].
Probab=27.02 E-value=1.2e+02 Score=16.68 Aligned_cols=18 Identities=33% Similarity=0.453 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy648 48 LAVLNEKLTTLERRIEYL 65 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~L 65 (72)
|-+++.||+.|..++.-|
T Consensus 17 L~R~E~kld~L~~~i~~L 34 (38)
T PF12841_consen 17 LVRIEKKLDELTESINEL 34 (38)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 334444444444444433
No 198
>PF03285 Paralemmin: Paralemmin; InterPro: IPR004965 Paralemmin was identified in the chicken lens as a protein with a molecular weight of 65 kDa (isoform 1) and a splice variant of 60 kDa (isoform 2). Isoform 2 is predominant during infancy and levels of isoform 1 increase with age. Paralemmin is localised to the plasma membrane of fibre cells, and was not detected in the annular pad cells. Its localisation to the short side of the fibre cell and the sites of fibre cell interlocking suggests that paralemmin may play a role in the development of such interdigitating processes []. Palmitoylation is important for localising these proteins to the filopodia of dendritic cells where they have been implicated in the regulation of membrane dynamics and process outgrowth. ; GO: 0008360 regulation of cell shape, 0016020 membrane
Probab=26.52 E-value=90 Score=23.97 Aligned_cols=24 Identities=33% Similarity=0.469 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
+.|--.|++-|.+||..|+.||.-
T Consensus 9 EqKtR~LEesI~RLEkEIe~LE~~ 32 (278)
T PF03285_consen 9 EQKTRSLEESIHRLEKEIEALENG 32 (278)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccC
Confidence 346678999999999999999964
No 199
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=26.35 E-value=2.2e+02 Score=19.54 Aligned_cols=41 Identities=22% Similarity=0.298 Sum_probs=26.2
Q ss_pred HHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 30 IKKITDFLNS----FDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 30 I~~~~~FLN~----F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
+..|..+|+. ....-+.++..++++++.|......|++.+.
T Consensus 61 L~eI~~ll~~~~~~~~~~L~~~~~~l~~ei~~L~~~~~~l~~ll~ 105 (172)
T cd04790 61 LEDIRSLLQQPGDDATDVLRRRLAELNREIQRLRQQQRAIATLLK 105 (172)
T ss_pred HHHHHHHHhcCChhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444442 2334567788888888888888777777653
No 200
>COG1590 Uncharacterized conserved protein [Function unknown]
Probab=26.34 E-value=2.3e+02 Score=21.06 Aligned_cols=36 Identities=28% Similarity=0.324 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 35 DFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 35 ~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
++|.--...|-++|...-+||..|+..|+-|..+.+
T Consensus 161 eyl~~lv~~~n~~l~r~k~kl~rl~~~le~l~~~~~ 196 (208)
T COG1590 161 EYLKFLVEIANEKLRRGKEKLARLEERLEELVEKCM 196 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 344444567788888888888888888887776543
No 201
>PRK06664 fliD flagellar hook-associated protein FliD; Validated
Probab=26.31 E-value=2.5e+02 Score=23.81 Aligned_cols=43 Identities=23% Similarity=0.420 Sum_probs=0.0
Q ss_pred HHhHHHHHHHHHHHH----------HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 27 TGSIKKITDFLNSFD----------MSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 27 n~~I~~~~~FLN~F~----------~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
+.+..++-++|+.+- .+-...+..++.++..+|++|+-+|.++
T Consensus 578 ~Gla~~l~~~l~~~t~~~G~i~~r~~~l~~~i~~l~~~i~~~e~rl~~~e~rl 630 (661)
T PRK06664 578 NGVAKMLLEYLSPYTQAGGIIYNKVKGLDERIADNNKKIEEYEKKLESKERKL 630 (661)
T ss_pred CcHHHHHHHHHHHHHcCCCceehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 202
>smart00189 IL2 Interleukin-2 family. Interleukin-2 is a cytokine produced by T-helper cells in response to antigenic or mitogenic stimulation. This protein is required for T-cell proliferation and other activities crucial to the regulation of the immune response.
Probab=26.30 E-value=65 Score=22.93 Aligned_cols=34 Identities=26% Similarity=0.495 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHhHH------------------HHHHHHHHHHHHHHHHHHHH
Q psy648 18 ANREYIEIITGSIK------------------KITDFLNSFDMSCRSRLAVL 51 (72)
Q Consensus 18 ~nRe~i~~in~~I~------------------~~~~FLN~F~~sc~~kLa~l 51 (72)
+.+++|.-||--+. .+|+|||+.-.-|.+=++++
T Consensus 102 ~~k~~isNInvtvl~LKGSet~f~CeydDet~tivEFLn~WItfCQsi~st~ 153 (154)
T smart00189 102 HIKDFISNINVTVLKLKGSETRFTCQYDDESVTIVEFLNRWIAFCQSIISTL 153 (154)
T ss_pred hHHHHHhhhhheeeeeccCCccceeeccCceehHHHHHHHHHHHHHHHHHcc
Confidence 35677777765443 58999999999998876653
No 203
>PF12507 HCMV_UL139: Human Cytomegalovirus UL139 protein; InterPro: IPR021042 This entry represents eukaryotic and viral proteins of approximately 140 amino acids in length. The UL139 product shares sequence homology with human CD24, a signal transducer modulating B-cell activation responses, and the sequences in the G1c variant of UL139 contained a specific attachment site of prokaryotic membrane lipoprotein lipid [].
Probab=26.06 E-value=1.1e+02 Score=21.07 Aligned_cols=28 Identities=29% Similarity=0.296 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.++.|++.+|-|+..+-..++-|+||-.
T Consensus 34 ~L~rKia~~~~~~l~~rs~i~~~~~k~~ 61 (121)
T PF12507_consen 34 LLERKIADQNFKILALRSEIEALDAKYH 61 (121)
T ss_pred HHHHHHHHHHHHHHHHhhhhhhhhhhhc
Confidence 4678999999999999999999998743
No 204
>COG5521 Predicted integral membrane protein [Function unknown]
Probab=26.00 E-value=1.6e+02 Score=22.76 Aligned_cols=38 Identities=16% Similarity=0.362 Sum_probs=28.3
Q ss_pred hHHHHHHHHHhhh--HHHHHHHHHHHhHHHHHHHHHHHHH
Q psy648 5 HREAIQKQIQQDW--ANREYIEIITGSIKKITDFLNSFDM 42 (72)
Q Consensus 5 ~~~~v~~~iq~DW--~nRe~i~~in~~I~~~~~FLN~F~~ 42 (72)
..++|...|.+|| +||-+|-..=........+|+.|-.
T Consensus 155 sv~sv~d~is~qWy~qnka~i~lflvl~~s~i~~l~tfiv 194 (275)
T COG5521 155 SVHSVEDLISTQWYAQNKAMIMLFLVLVVSMIQLLLTFIV 194 (275)
T ss_pred chhHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999 6777776666666666677777653
No 205
>PRK11239 hypothetical protein; Provisional
Probab=25.91 E-value=1.4e+02 Score=22.36 Aligned_cols=21 Identities=24% Similarity=0.333 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q psy648 49 AVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 49 a~ln~KL~~LE~~L~~LEAkl 69 (72)
..|++++..||..+.-|+++|
T Consensus 186 ~~Le~rv~~Le~eva~L~~~l 206 (215)
T PRK11239 186 GDLQARVEALEIEVAELKQRL 206 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555555554443
No 206
>smart00338 BRLZ basic region leucin zipper.
Probab=25.85 E-value=1.4e+02 Score=17.05 Aligned_cols=22 Identities=27% Similarity=0.314 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q psy648 48 LAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 48 La~ln~KL~~LE~~L~~LEAkl 69 (72)
+..|+.+++.|+....-|.+++
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~ 49 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEI 49 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555544444443
No 207
>COG4476 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.84 E-value=48 Score=21.80 Aligned_cols=30 Identities=20% Similarity=0.584 Sum_probs=22.0
Q ss_pred HhhhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q psy648 14 QQDWANREYIEIITGSIKKITDFLNSFDMSCRSRLAVL 51 (72)
Q Consensus 14 q~DW~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~l 51 (72)
--||.+-|++.+| .|+|.-+.-.+.+....
T Consensus 8 dldWsTEE~~~Vl--------~Ffn~VE~aYE~gv~~~ 37 (90)
T COG4476 8 DLDWSTEEMISVL--------HFFNAVELAYEKGVDAE 37 (90)
T ss_pred CCCccHHHHHHHH--------HHHHHHHHHHHccccHH
Confidence 4599999998776 47787777777666543
No 208
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=25.83 E-value=1.2e+02 Score=18.35 Aligned_cols=23 Identities=43% Similarity=0.520 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy648 45 RSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 45 ~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
..++..++++|..|+.++.-++.
T Consensus 4 g~~l~~l~~~l~~l~~~~~~~~~ 26 (70)
T PF10975_consen 4 GQRLAELEQQLKQLEDQQEELEQ 26 (70)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHc
Confidence 35677777777777777766653
No 209
>KOG1419|consensus
Probab=25.69 E-value=90 Score=26.83 Aligned_cols=23 Identities=26% Similarity=0.556 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYL 65 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~L 65 (72)
|.=.||..++.+.++||++|+.|
T Consensus 566 Sm~~Rl~~vEkqv~~le~Kld~l 588 (654)
T KOG1419|consen 566 SMMGRLVKVEKQVQSLEKKLDLL 588 (654)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 45567888888888888888765
No 210
>TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit. This model represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. This model must be designated subfamily to indicate the heterogeneity of PHAs.
Probab=25.43 E-value=3.3e+02 Score=21.30 Aligned_cols=53 Identities=19% Similarity=0.226 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 18 ANREYIEIITGSIKKITDFLNSFDMS-----------CRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 18 ~nRe~i~~in~~I~~~~~FLN~F~~s-----------c~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.+-||...+..++-...++-..+... +|+=+.++..+|..|||++.-|+..|.
T Consensus 250 ~S~efak~~G~lvna~m~lr~~~qe~~e~~L~~LnlPTRsElDe~~krL~ELrR~vr~L~k~l~ 313 (320)
T TIGR01834 250 ASEENAKVHGKFINALMRLRIQQQEIVEALLKMLNLPTRSELDEAHQRIQQLRREVKSLKKRLG 313 (320)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34577777777777777776666554 455566677888888888888877764
No 211
>TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit. This model represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. This model must be designated subfamily to indicate the heterogeneity of PHAs.
Probab=25.42 E-value=91 Score=24.38 Aligned_cols=26 Identities=27% Similarity=0.487 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.-.+|..|+.++..|++.|.-||+++
T Consensus 294 ~~krL~ELrR~vr~L~k~l~~l~~~~ 319 (320)
T TIGR01834 294 AHQRIQQLRREVKSLKKRLGDLEANP 319 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcC
Confidence 44689999999999999999999875
No 212
>PRK14064 exodeoxyribonuclease VII small subunit; Provisional
Probab=25.38 E-value=83 Score=19.40 Aligned_cols=18 Identities=11% Similarity=0.453 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy648 41 DMSCRSRLAVLNEKLTTL 58 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~L 58 (72)
...|+.+|...+.|++.|
T Consensus 43 ~k~c~~~L~~ae~kv~~l 60 (75)
T PRK14064 43 TKLCQDKLQSAEKRMAKV 60 (75)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 346888888888777754
No 213
>PRK05892 nucleoside diphosphate kinase regulator; Provisional
Probab=25.27 E-value=80 Score=21.72 Aligned_cols=19 Identities=32% Similarity=0.524 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHhhcc
Q psy648 53 EKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 53 ~KL~~LE~~L~~LEAklss 71 (72)
+++..+|+++.+||.+|++
T Consensus 54 ~~q~~~e~RI~~L~~~L~~ 72 (158)
T PRK05892 54 DELARLDDRINELDRRLRT 72 (158)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 4455666677777666653
No 214
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=25.18 E-value=74 Score=24.13 Aligned_cols=17 Identities=35% Similarity=0.630 Sum_probs=8.8
Q ss_pred HHHHHHHHHHHHHHhhc
Q psy648 54 KLTTLERRIEYLEARKS 70 (72)
Q Consensus 54 KL~~LE~~L~~LEAkls 70 (72)
++..|+.+++.|+|++.
T Consensus 82 ~l~~Lq~ql~~l~akI~ 98 (258)
T PF15397_consen 82 KLSKLQQQLEQLDAKIQ 98 (258)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34445555555555553
No 215
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=25.12 E-value=1.9e+02 Score=18.26 Aligned_cols=29 Identities=17% Similarity=0.122 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 41 DMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
...-+.++..+++++..|.+....|+..+
T Consensus 81 ~~~l~~~~~~l~~~i~~l~~~~~~l~~~~ 109 (123)
T cd04770 81 RALLEEKLAEVEAKIAELQALRAELAGLL 109 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567888899998888888888887655
No 216
>PRK13710 plasmid maintenance protein CcdA; Provisional
Probab=25.08 E-value=1.4e+02 Score=18.40 Aligned_cols=34 Identities=18% Similarity=0.331 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhh--HHHHHHHHHHHhHHHHHHHHHH
Q psy648 6 REAIQKQIQQDW--ANREYIEIITGSIKKITDFLNS 39 (72)
Q Consensus 6 ~~~v~~~iq~DW--~nRe~i~~in~~I~~~~~FLN~ 39 (72)
.+.+.+.-.+-| +|||-|+-+|.||-.==-|+..
T Consensus 33 ~~~~~~~~~~~W~~eN~eai~~~n~~ve~~G~~~de 68 (72)
T PRK13710 33 QNEARRLRAERWKAENREGMAEVARFIEMNGSFADE 68 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcHHh
Confidence 455666777889 5999999999999765444443
No 217
>PF12958 DUF3847: Protein of unknown function (DUF3847); InterPro: IPR024215 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=24.98 E-value=1.9e+02 Score=18.45 Aligned_cols=30 Identities=27% Similarity=0.288 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 37 LNSFDMSCRSRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 37 LN~F~~sc~~kLa~ln~KL~~LE~~L~~LE 66 (72)
|+.=-...+.||....+++..|+.+.-.|+
T Consensus 6 l~~e~e~~~~kl~q~e~~~k~L~nr~k~l~ 35 (86)
T PF12958_consen 6 LQAEIEKAEKKLEQAEHKIKQLENRKKKLE 35 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344567888888888888888888887
No 218
>PRK00977 exodeoxyribonuclease VII small subunit; Provisional
Probab=24.75 E-value=93 Score=19.29 Aligned_cols=18 Identities=17% Similarity=0.486 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy648 41 DMSCRSRLAVLNEKLTTL 58 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~L 58 (72)
...|+.+|...+.|++.|
T Consensus 47 ~k~C~~~L~~ae~ki~~l 64 (80)
T PRK00977 47 ARQCQKKLQQAEQRVEKL 64 (80)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 346888887777777766
No 219
>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 [].
Probab=24.68 E-value=1.3e+02 Score=19.26 Aligned_cols=20 Identities=35% Similarity=0.476 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q psy648 47 RLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 47 kLa~ln~KL~~LE~~L~~LE 66 (72)
.+..+++|++.+|..++-||
T Consensus 9 ~~~~~~~ki~~ve~~V~~l~ 28 (116)
T PF10552_consen 9 ATEEHNEKIEEVENRVDDLE 28 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34556667777776666665
No 220
>PRK04387 hypothetical protein; Provisional
Probab=24.56 E-value=49 Score=21.58 Aligned_cols=17 Identities=24% Similarity=0.554 Sum_probs=13.0
Q ss_pred HHhhhHHHHHHHHHHHh
Q psy648 13 IQQDWANREYIEIITGS 29 (72)
Q Consensus 13 iq~DW~nRe~i~~in~~ 29 (72)
|--||.+-|++.+|+.|
T Consensus 7 ld~dWsteEii~Vi~F~ 23 (90)
T PRK04387 7 LDLDWSTEEMISVLHFF 23 (90)
T ss_pred CCCCCCHHHHHHHHHHH
Confidence 34699999999887644
No 221
>PF00517 GP41: Retroviral envelope protein; InterPro: IPR000328 This entry represents envelope proteins from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from Human immunodeficiency virus (HIV) and Simian-Human immunodeficiency virus (SIV), which mediate membrane fusion during viral entry []. It has a core composed of a six-helix bundle and is folded by its trimeric N- and C-terminal heptad-repeats (NHR and CHR) []. Derivatives of this protein prevent HIV-1 from entering cell lines and primary human CD4+ cells in vitro [], making it an attractive subject of gene therapy studies against HIV and related retroviruses. The entry also represents envelop proteins from Bovine immunodeficiency virus, Feline immunodeficiency virus and Equine infectious anemia virus (EIAV) [, ], as well as the Gp36 protein from Mouse mammary tumor virus (MMTV) and Human endogenous retrovirus (HERV).; GO: 0005198 structural molecule activity, 0019031 viral envelope; PDB: 2EZO_B 2EZQ_B 2EZR_A 2JNR_B 1F23_D 2EZP_A 1JEK_A 2Q7C_A 2Q5U_A 2Q3I_A ....
Probab=24.23 E-value=2.7e+02 Score=19.81 Aligned_cols=51 Identities=10% Similarity=0.050 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 19 NREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 19 nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.|++++.+.....++.+=.......-+..+-.++..+..|.+++..||..+
T Consensus 12 ~~~~l~~i~q~~~~ll~~~e~~~~lL~l~v~gik~~V~~L~aRV~alE~~l 62 (204)
T PF00517_consen 12 SAQLLNGIVQQQSNLLRAQEAQQHLLQLTVWGIKQGVKQLQARVLALERYL 62 (204)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 567888888888888877777777767666666665555666666665544
No 222
>PF14805 THDPS_N_2: Tetrahydrodipicolinate N-succinyltransferase N-terminal; PDB: 3EG4_A 3TDT_A 2TDT_A 1KGT_A 1TDT_A 1KGQ_A 3BXY_A 3GOS_A 3TK8_A.
Probab=24.20 E-value=1e+02 Score=18.89 Aligned_cols=18 Identities=33% Similarity=0.693 Sum_probs=14.1
Q ss_pred HHHHHHHHhhhHHHHHHH
Q psy648 7 EAIQKQIQQDWANREYIE 24 (72)
Q Consensus 7 ~~v~~~iq~DW~nRe~i~ 24 (72)
++++..|.+-|++|+-+.
T Consensus 1 ~~l~~~Ie~aw~~r~~l~ 18 (70)
T PF14805_consen 1 SQLQKIIEAAWENRDELT 18 (70)
T ss_dssp HHHHHHHHHHHHGGGG-B
T ss_pred ChHHHHHHHHHHhHhhCC
Confidence 367889999999998774
No 223
>PF05549 Allexi_40kDa: Allexivirus 40kDa protein; InterPro: IPR008398 This family of sequences contains the 40 kDa polypeptides from garlic viruses (Allexiviruses), which do not resemble any other plant virus gene products reported so far []. Rod-shaped flexuous viruses have been isolated from garlic plants, Allium sativum. Infection by this virus creates typical mosaic symptoms. The core-like sequence of a zinc finger protein preceded by a cluster of basic amino acid residues shows similarities to the corresponding 12K proteins of the potexviruses and carlaviruses []. Viral epidemics by allexiviruses are also known to be caused by aphids and eriophyid mites (Aceria tulipae) carrying Potyviruses, Carlaviruses, and Allexiviruses [].
Probab=24.10 E-value=1.5e+02 Score=22.95 Aligned_cols=21 Identities=24% Similarity=0.570 Sum_probs=17.0
Q ss_pred HHHHHHHHhHHHHHHHHHHHH
Q psy648 21 EYIEIITGSIKKITDFLNSFD 41 (72)
Q Consensus 21 e~i~~in~~I~~~~~FLN~F~ 41 (72)
|-+-.|||++-.|.+.||-|.
T Consensus 52 EWLTHI~h~~d~ii~~ln~~~ 72 (271)
T PF05549_consen 52 EWLTHINHNVDQIINMLNPIN 72 (271)
T ss_pred HHHHhcCccHHHHHHHhCccc
Confidence 567788888888888888883
No 224
>COG0732 HsdS Restriction endonuclease S subunits [Defense mechanisms]
Probab=23.74 E-value=2.7e+02 Score=19.58 Aligned_cols=39 Identities=21% Similarity=0.331 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 30 IKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 30 I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
..+++++|..++.-|...... .+++..+|....++-.++
T Consensus 349 Q~~i~~~l~~l~~~i~~~~~~-~~~~~~~~~~~~~~l~~l 387 (391)
T COG0732 349 QQKIAEILSALDKLIDILNRK-PAELEALKKQLDYLLNKL 387 (391)
T ss_pred HHHHHHHHHHHHHHHHHhhcc-HHHHHHHHHHHHHHHHHh
Confidence 456777888887766665555 557788888777665554
No 225
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=23.64 E-value=2.1e+02 Score=18.53 Aligned_cols=46 Identities=22% Similarity=0.277 Sum_probs=30.6
Q ss_pred HHHHHhhhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 10 QKQIQQDWANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLE 59 (72)
Q Consensus 10 ~~~iq~DW~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE 59 (72)
..-+.+-|+.| -++.-..++.+++++|+..--+.-..+=+.|-.++
T Consensus 18 ~~iL~~~~~~~----els~~~~ktl~y~~kFsk~~~e~a~elve~L~~~~ 63 (112)
T PRK14981 18 KEILSEIEEER----ELSYELRRTLDYLNRFSKLDPEDAEELVEELLELE 63 (112)
T ss_pred HHHHHHHHhcc----chhHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcc
Confidence 34445556666 55667889999999999776555555555554433
No 226
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.58 E-value=1.9e+02 Score=17.78 Aligned_cols=36 Identities=25% Similarity=0.409 Sum_probs=24.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 29 SIKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 29 ~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
.|..|.++++.- +......|+++++.++.++.-|+.
T Consensus 59 ~l~~I~~~l~~~---~~~~~~~l~~~~~~l~~~i~~l~~ 94 (96)
T cd04768 59 SLAEIKELLDTE---MEELTAMLLEKKQAIQQKIDRLQQ 94 (96)
T ss_pred CHHHHHHHHhcC---cHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455566666542 336777788888888888887764
No 227
>PF07426 Dynactin_p22: Dynactin subunit p22; InterPro: IPR009991 This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localises to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis [].
Probab=23.51 E-value=82 Score=22.17 Aligned_cols=15 Identities=40% Similarity=0.851 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHHHH
Q psy648 48 LAVLNEKLTTLERRI 62 (72)
Q Consensus 48 La~ln~KL~~LE~~L 62 (72)
|..|+.||+.||+++
T Consensus 7 l~~Le~Ri~~LE~~v 21 (174)
T PF07426_consen 7 LDILEKRIEELERRV 21 (174)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344444444444444
No 228
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=23.49 E-value=1.8e+02 Score=17.61 Aligned_cols=34 Identities=29% Similarity=0.360 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 37 LNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 37 LN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
|..=..--+.-+..+..++..+|..+.-|+.+++
T Consensus 38 Lr~~~~e~e~~~~~l~~~~~~~e~~~~~l~~~l~ 71 (74)
T PF12329_consen 38 LRAKIKELEKQIKELKKKLEELEKELESLEERLK 71 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4444445566777778888888888888877765
No 229
>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....
Probab=23.45 E-value=2.8e+02 Score=19.77 Aligned_cols=27 Identities=33% Similarity=0.471 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.-+.++..|..+|...|.+.+..|.++
T Consensus 173 ~~e~~i~~L~~~lkeaE~Rae~aE~~v 199 (237)
T PF00261_consen 173 EYEEKIRDLEEKLKEAENRAEFAERRV 199 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555566666666555555555544
No 230
>PF01420 Methylase_S: Type I restriction modification DNA specificity domain; InterPro: IPR000055 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. This entry represents the S subunit of type I restriction endonucleases (3.1.21.3 from EC). The M and S subunits together form a methyltransferase that methylates two adenine residues in complementary strands of a bipartite DNA recognition sequence. In the presence of the R subunit the complex can also act as an endonuclease, binding to the same target sequence but cutting the DNA some distance from this site. Whether the DNA is cut or modified depends on the methylation state of the target sequence: when the target site is unmodified, the DNA is cut; when the target site is hemi-methylated, the complex acts as a maintenance methyltransferase to modify the DNA, methylating both strands []. Most of the proteins in this family have two copies of the domain.; GO: 0003677 DNA binding, 0006304 DNA modification; PDB: 1YF2_B 2Y7H_A 2Y7C_A 3OKG_A 1YDX_A.
Probab=23.43 E-value=1.8e+02 Score=17.79 Aligned_cols=11 Identities=36% Similarity=0.685 Sum_probs=5.8
Q ss_pred HHHHHHHHHHH
Q psy648 32 KITDFLNSFDM 42 (72)
Q Consensus 32 ~~~~FLN~F~~ 42 (72)
.++++|++++.
T Consensus 143 ~i~~~l~~~~~ 153 (167)
T PF01420_consen 143 KIVEILDQLDK 153 (167)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 45555555553
No 231
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=23.40 E-value=1.8e+02 Score=17.48 Aligned_cols=21 Identities=29% Similarity=0.621 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy648 43 SCRSRLAVLNEKLTTLERRIE 63 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~ 63 (72)
.++.++..++.+++.+..++.
T Consensus 68 ~ikkrm~~l~~~l~~lk~R~~ 88 (92)
T PF14712_consen 68 NIKKRMSNLHERLQKLKKRAD 88 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 345555555555555555544
No 232
>PRK11239 hypothetical protein; Provisional
Probab=23.07 E-value=1.3e+02 Score=22.51 Aligned_cols=27 Identities=22% Similarity=0.383 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
=+.+++.|+.++..|++.++-|.+++.
T Consensus 188 Le~rv~~Le~eva~L~~~l~~l~~~~~ 214 (215)
T PRK11239 188 LQARVEALEIEVAELKQRLDSLLAHLG 214 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 578899999999999999999888775
No 233
>PRK14070 exodeoxyribonuclease VII small subunit; Provisional
Probab=22.93 E-value=1e+02 Score=18.93 Aligned_cols=19 Identities=16% Similarity=0.170 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q psy648 41 DMSCRSRLAVLNEKLTTLE 59 (72)
Q Consensus 41 ~~sc~~kLa~ln~KL~~LE 59 (72)
...|+.+|...+.|++.+=
T Consensus 32 ~k~C~~~L~~aE~kI~~l~ 50 (69)
T PRK14070 32 YRKCKEILQQNRLKIIDVM 50 (69)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3578888888888877653
No 234
>PF09823 DUF2357: Domain of unknown function (DUF2357); InterPro: IPR018633 This entry was previously the N-terminal portion of DUF524 (IPR007505 from INTERPRO) before it was split into two. This domain has no known function. It is predicted to adopt an all beta secondary structure pattern followed by mainly alpha-helical structures [].
Probab=22.87 E-value=2.6e+02 Score=19.23 Aligned_cols=17 Identities=6% Similarity=0.229 Sum_probs=8.7
Q ss_pred HHHHhHHHHHHHHHHHH
Q psy648 25 IITGSIKKITDFLNSFD 41 (72)
Q Consensus 25 ~in~~I~~~~~FLN~F~ 41 (72)
||-+++.++..+|+++.
T Consensus 168 fvK~~L~~~~~~l~~l~ 184 (248)
T PF09823_consen 168 FVKYFLQRLEKRLERLK 184 (248)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 44455555555555443
No 235
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=22.79 E-value=2e+02 Score=23.76 Aligned_cols=24 Identities=8% Similarity=0.041 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 46 SRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.+...+++||..+|..+.-|++++
T Consensus 97 aq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 97 KQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHH
Confidence 344455555556666666665554
No 236
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=22.62 E-value=2e+02 Score=17.74 Aligned_cols=24 Identities=25% Similarity=0.416 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 47 RLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 47 kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
....+..++..+|..+.-+|.++.
T Consensus 75 e~~~lk~~i~~le~~~~~~e~~l~ 98 (108)
T PF02403_consen 75 EVKELKEEIKELEEQLKELEEELN 98 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677777888888877777653
No 237
>PRK14067 exodeoxyribonuclease VII small subunit; Provisional
Probab=22.48 E-value=1e+02 Score=19.32 Aligned_cols=18 Identities=22% Similarity=0.490 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy648 42 MSCRSRLAVLNEKLTTLE 59 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE 59 (72)
..|+.+|...+.|++.|.
T Consensus 45 k~C~~~L~~ae~kI~~l~ 62 (80)
T PRK14067 45 RACREQLAKARNEIRLFT 62 (80)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 468888777777776653
No 238
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=22.45 E-value=2e+02 Score=18.48 Aligned_cols=23 Identities=22% Similarity=0.224 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q psy648 46 SRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
.+++.++.+++.++.+-..|+.+
T Consensus 34 ~q~~~~~~e~~~l~~~n~~L~~e 56 (105)
T PRK00888 34 DQVAAQQQTNAKLKARNDQLFAE 56 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444444443
No 239
>PF14063 DUF4254: Protein of unknown function (DUF4254)
Probab=22.44 E-value=2.3e+02 Score=19.45 Aligned_cols=29 Identities=34% Similarity=0.465 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
.|..||..++++...|-+.++-|=.-+..
T Consensus 110 ~~~~kl~vl~~qradL~~~i~~Ll~d~~~ 138 (145)
T PF14063_consen 110 RCARKLYVLNEQRADLKRAIDQLLGDILA 138 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 68899999999999999988877554443
No 240
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=22.42 E-value=2.4e+02 Score=18.49 Aligned_cols=27 Identities=30% Similarity=0.375 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHH----HHHHHHHHHHhh
Q psy648 43 SCRSRLAVLNEKLTT----LERRIEYLEARK 69 (72)
Q Consensus 43 sc~~kLa~ln~KL~~----LE~~L~~LEAkl 69 (72)
.=+++|..|.+||.. -+..|+-||..+
T Consensus 69 ~EkEqL~~Lk~kl~~e~~~~~k~i~~le~~I 99 (100)
T PF04568_consen 69 KEKEQLKKLKEKLKEEIEHHRKEIDELEKHI 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 345677777777777 677777777655
No 241
>PRK12765 flagellar capping protein; Provisional
Probab=22.32 E-value=1.6e+02 Score=24.50 Aligned_cols=34 Identities=15% Similarity=0.174 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 37 LNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 37 LN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
|.....+-...+..|+++...++++|+-+|+++.
T Consensus 530 l~~~~~~l~~~~~~l~~~~~~~~~rl~~~~~r~~ 563 (595)
T PRK12765 530 LTKYDESLTNEIKSLTTSKESTQELIDTKYETMA 563 (595)
T ss_pred chhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444556666777777777777777777777654
No 242
>PF09177 Syntaxin-6_N: Syntaxin 6, N-terminal; InterPro: IPR015260 Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport []. ; GO: 0048193 Golgi vesicle transport, 0016020 membrane; PDB: 1LVF_B 2C5I_T 2C5J_A 2C5K_T 4DND_A.
Probab=22.29 E-value=1.6e+02 Score=18.17 Aligned_cols=25 Identities=24% Similarity=0.341 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 43 SCRSRLAVLNEKLTTLERRIEYLEA 67 (72)
Q Consensus 43 sc~~kLa~ln~KL~~LE~~L~~LEA 67 (72)
--++-|.+++.-|..||+++.+.|+
T Consensus 43 eL~~~l~~ie~~L~DL~~aV~ive~ 67 (97)
T PF09177_consen 43 ELRNALQSIEWDLEDLEEAVRIVEK 67 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3345556677777777777777664
No 243
>PF00715 IL2: Interleukin 2 This family is a subset of the SCOP family.; InterPro: IPR000779 T-Lymphocytes regulate the growth and differentiation of certain lymphopoietic and haemopoietic cells through the release of various secreted protein factors []. These factors, which include interleukin-2 (IL2), are secreted by lectin- or antigen-stimulated T-cells, and have various physiological effects. IL2 is a lymphokine that induces the proliferation of responsive T-cells. In addition, it acts on some B-cells, via receptor-specific binding [], as a growth factor and antibody production stimulant []. The protein is secreted as a single glycosylated polypeptide, and cleavage of a signal sequence is required for its activity []. Solution NMR suggests that the structure of IL2 comprises a bundle of 4 helices (termed A-D), flanked by 2 shorter helices and several poorly-defined loops. Residues in helix A, and in the loop region between helices A and B, are important for receptor binding. Secondary structure analysis has suggested similarity to IL4 and granulocyte-macrophage colony stimulating factor (GMCSF) [].; GO: 0005134 interleukin-2 receptor binding, 0008083 growth factor activity, 0006955 immune response, 0005576 extracellular region; PDB: 3QAZ_M 2B5I_A 1Z92_A 3QB1_F 2ERJ_H 1NBP_A 1PY2_C 1IRL_A 1QVN_A 3INK_C ....
Probab=22.28 E-value=1.1e+02 Score=21.73 Aligned_cols=30 Identities=33% Similarity=0.450 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhHHH------------------HHHHHHHHHHHHHHH
Q psy648 18 ANREYIEIITGSIKK------------------ITDFLNSFDMSCRSR 47 (72)
Q Consensus 18 ~nRe~i~~in~~I~~------------------~~~FLN~F~~sc~~k 47 (72)
+.+++|.-||--+.+ +|+|||++=.-|.+=
T Consensus 96 ~~~~~isNInvtv~~LkGset~f~Ceyddet~tiveFln~WItFCQsi 143 (145)
T PF00715_consen 96 DIKESISNINVTVLKLKGSETTFTCEYDDETVTIVEFLNKWITFCQSI 143 (145)
T ss_dssp H-HHHHHHHHHHHHHHH-SSS-S---BESSEBEHHHHHHHHHHHHHHH
T ss_pred cHHHHHHhhhHhhhhccCCCccceeeccCceehHHHHHHHHHHHHHHh
Confidence 457888888876653 799999999999764
No 244
>PF11435 She2p: RNA binding protein She2p; InterPro: IPR024261 She2p is a RNA binding protein which binds to RNA via a helical hairpin. The protein is required for the actin dependent transport of ASH1 mRNA in yeast, a form of mRNP translocation []. She2p contains a globular domain consisting of a bundle of five alpha-helices []. This entry represents the main structural domain of She2p.; GO: 0003723 RNA binding; PDB: 1XLY_A.
Probab=22.26 E-value=1.3e+02 Score=22.46 Aligned_cols=25 Identities=32% Similarity=0.384 Sum_probs=19.5
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHH
Q psy648 21 EYIEIITGSIKKITDFLNSFDMSCR 45 (72)
Q Consensus 21 e~i~~in~~I~~~~~FLN~F~~sc~ 45 (72)
+.++..+-+|.+=+++||+|=..-|
T Consensus 5 e~i~~fs~YiS~yI~~LNkfI~~lR 29 (204)
T PF11435_consen 5 EIIELFSKYISSYIHLLNKFIGHLR 29 (204)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677778888888899999876544
No 245
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=22.00 E-value=2.4e+02 Score=18.44 Aligned_cols=53 Identities=23% Similarity=0.263 Sum_probs=30.5
Q ss_pred hHHHHHHHHHhhhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 5 HREAIQKQIQQDWANREYIEIITGSIKKITDFLNSFDMSCRSRLAVLNEKLTTLERR 61 (72)
Q Consensus 5 ~~~~v~~~iq~DW~nRe~i~~in~~I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~ 61 (72)
+++.+.--.-+||.=.|+.+..+-.-.-+.+-+.+ |+.+|..+++||.-+++.
T Consensus 22 Q~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr----~~~~L~~yE~kL~l~~k~ 74 (101)
T PF04297_consen 22 QREILELYYEEDLSLSEIAEELGISRQAVYDSIKR----AEKKLEEYEEKLGLVEKF 74 (101)
T ss_dssp HHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHH----HHHHHHHHHHHH-HHHHH
T ss_pred HHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHhhHHHH
Confidence 45556666677888888887766555555555543 666666666666666544
No 246
>PF11944 DUF3461: Protein of unknown function (DUF3461); InterPro: IPR020911 This entry describes proteins of unknown function.
Probab=21.57 E-value=1.6e+02 Score=20.34 Aligned_cols=25 Identities=24% Similarity=0.353 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 33 ITDFLNSFDMSCRSRLAVLNEKLTT 57 (72)
Q Consensus 33 ~~~FLN~F~~sc~~kLa~ln~KL~~ 57 (72)
+.+=|-.++.+.-+|++.++.+|.+
T Consensus 100 iL~dL~HLE~Vv~~KIaEIe~dlek 124 (125)
T PF11944_consen 100 ILDDLRHLEKVVNSKIAEIERDLEK 124 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3444555555555666555555443
No 247
>PF12761 End3: Actin cytoskeleton-regulatory complex protein END3
Probab=21.48 E-value=1.3e+02 Score=22.02 Aligned_cols=25 Identities=32% Similarity=0.466 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 47 RLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 47 kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
-|..+.+-|+.+|.+++.||.-|++
T Consensus 161 ~l~~v~~Dl~~ie~QV~~Le~~L~~ 185 (195)
T PF12761_consen 161 NLKSVREDLDTIEEQVDGLESHLSS 185 (195)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555667799999999999988764
No 248
>PF08537 NBP1: Fungal Nap binding protein NBP1; InterPro: IPR013743 NBP1 is a nuclear protein which has been shown in Saccharomyces cerevisiae (Bakers yeast) to be essential for the G2/M transition of the cell cycle.
Probab=21.46 E-value=1.7e+02 Score=23.09 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 46 SRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.|+..|+++|..+|..|+++-.+|
T Consensus 182 kk~~~l~~~l~~~~~eL~~~~k~L 205 (323)
T PF08537_consen 182 KKIDELEERLNDLEKELEITKKDL 205 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666666666666666655544
No 249
>KOG4090|consensus
Probab=21.40 E-value=2.2e+02 Score=20.44 Aligned_cols=33 Identities=6% Similarity=0.115 Sum_probs=27.3
Q ss_pred hhhHHHHHHHHHHHh--HHHHHHHHHHHHHHHHHH
Q psy648 15 QDWANREYIEIITGS--IKKITDFLNSFDMSCRSR 47 (72)
Q Consensus 15 ~DW~nRe~i~~in~~--I~~~~~FLN~F~~sc~~k 47 (72)
=+|+-|.|++.++.+ =.++++|.|+--.-|+..
T Consensus 118 C~~e~kqF~dCa~~~~~d~slC~~f~e~Lk~Ck~~ 152 (157)
T KOG4090|consen 118 CFIEIKQFLDCAQNQGSDISLCEGYNEMLKQCKKN 152 (157)
T ss_pred hHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHH
Confidence 379999999999998 677888888887788753
No 250
>cd03202 GST_C_etherase_LigE GST_C family, Beta etherase LigE subfamily; composed of proteins similar to Sphingomonas paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using GSH as the hydrogen donor. This reaction is an essential step in the degradation of lignin, a complex phenolic polymer that is the most abundant aromatic material in the biosphere. The beta etherase activity of LigE is enantioselective and it complements the activity of the other GST family beta etherase, LigF. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains.
Probab=21.35 E-value=1.1e+02 Score=19.25 Aligned_cols=32 Identities=22% Similarity=0.145 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 40 FDMSCRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 40 F~~sc~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
|..+++.--.......+.+++.+..||..|+.
T Consensus 45 ~g~~le~~~~~~~~~~~~~~~~l~~l~~~L~~ 76 (124)
T cd03202 45 FGRSLEEVAAGREAALANFRAALEPLRATLKG 76 (124)
T ss_pred hCCCHHHHCcchHHHHHHHHHHHHHHHHHHcC
Confidence 44555555555667778899999999998865
No 251
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=21.31 E-value=1.5e+02 Score=17.55 Aligned_cols=22 Identities=14% Similarity=0.336 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q psy648 35 DFLNSFDMSCRSRLAVLNEKLT 56 (72)
Q Consensus 35 ~FLN~F~~sc~~kLa~ln~KL~ 56 (72)
+||+.-.-.|++..+.++...+
T Consensus 3 tFL~~IGR~~~~~~~kf~~~w~ 24 (57)
T PF09597_consen 3 TFLKLIGRGCEEHAEKFESDWE 24 (57)
T ss_pred HHHHHHcccHHHHHHHHHHHHH
Confidence 6777777777777666665443
No 252
>PF10444 Nbl1_Borealin_N: Nbl1 / Borealin N terminal; InterPro: IPR018851 This entry represents the N-terminal domain of borealin, and is also found in the N-terminal-Borealin-like (NBL; YHR199C-A) protein from Saccharomyces cerevisiae (Baker's yeast). NBL is a subunit of the conserved chromosomal passenger complex (CPC; Ipl1p-Sli15p-Bir1p-Nbl1p), which regulates mitotic chromosome segregation. It is not required for the kinase activity of the complex and it mediates the interaction of Sli15p and Bir1p [].; PDB: 2RAW_B 2RAX_Y 2QFA_B.
Probab=21.16 E-value=1.8e+02 Score=16.69 Aligned_cols=23 Identities=26% Similarity=0.554 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy648 34 TDFLNSFDMSCRSRLAVLNEKLT 56 (72)
Q Consensus 34 ~~FLN~F~~sc~~kLa~ln~KL~ 56 (72)
-.||++|+.-.+.|...+....+
T Consensus 4 ~~~l~~fd~Ev~~r~~~lr~~~~ 26 (59)
T PF10444_consen 4 QAFLQNFDLEVEERIRRLRAQYE 26 (59)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 35889998887777776664443
No 253
>PF05557 MAD: Mitotic checkpoint protein; InterPro: IPR008672 This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in Saccharomyces cerevisiae and higher eukaryotes. In Saccharomyces cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated [].; PDB: 1GO4_F 4DZO_A.
Probab=21.07 E-value=1.6e+02 Score=24.49 Aligned_cols=28 Identities=18% Similarity=0.268 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARKSH 71 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAklss 71 (72)
-+.++..|+..+..|+..+..||.+|.+
T Consensus 508 L~~~~~~Le~e~~~L~~~~~~Le~~l~~ 535 (722)
T PF05557_consen 508 LQKEIEELERENERLRQELEELESELEK 535 (722)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567888888888888888999988864
No 254
>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].
Probab=20.95 E-value=3.1e+02 Score=19.28 Aligned_cols=24 Identities=29% Similarity=0.300 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 46 SRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.....+..++..|+....-|+.++
T Consensus 120 ~~~~~l~~~i~~L~~e~~~L~~~~ 143 (189)
T PF10211_consen 120 QGKQELEEEIEELEEEKEELEKQV 143 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334555555555555555555544
No 255
>PRK14069 exodeoxyribonuclease VII small subunit; Provisional
Probab=20.77 E-value=1.1e+02 Score=19.96 Aligned_cols=18 Identities=22% Similarity=0.302 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHH
Q psy648 42 MSCRSRLAVLNEKLTTLE 59 (72)
Q Consensus 42 ~sc~~kLa~ln~KL~~LE 59 (72)
..|+.+|...+.|++.|-
T Consensus 46 k~C~~~L~~AE~kV~~L~ 63 (95)
T PRK14069 46 KICSGILDDAEGKIEALT 63 (95)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 468888888887777663
No 256
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.62 E-value=2.1e+02 Score=17.23 Aligned_cols=24 Identities=33% Similarity=0.484 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 47 RLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 47 kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.+..|.+++..|++.+.-|-.+++
T Consensus 66 ~~l~l~~~~~~l~~~l~~l~~~~~ 89 (91)
T cd04766 66 RILELEEELAELRAELDELRARLR 89 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344488888888888888877765
No 257
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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 su
Probab=20.60 E-value=2.6e+02 Score=18.37 Aligned_cols=26 Identities=12% Similarity=0.014 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Q psy648 44 CRSRLAVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 44 c~~kLa~ln~KL~~LE~~L~~LEAkl 69 (72)
.+.|++.+++++..|.+....|+..+
T Consensus 83 l~~k~~~i~~~i~~L~~~~~~L~~~i 108 (131)
T cd04786 83 LERKVADIEALEARLAQNKAQLLVLI 108 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555555555555443
No 258
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=20.58 E-value=3e+02 Score=18.93 Aligned_cols=49 Identities=8% Similarity=0.139 Sum_probs=35.4
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHhh
Q psy648 21 EYIEIITGSIKKITDFLNSFDMSCRSRL--AVLNEKLTTLERRIEYLEARK 69 (72)
Q Consensus 21 e~i~~in~~I~~~~~FLN~F~~sc~~kL--a~ln~KL~~LE~~L~~LEAkl 69 (72)
..=.|++..+-.+++-+++|..-.+.-. ....+.+...|..|+.|+..+
T Consensus 126 ~a~~Fl~~yLp~~~~l~~kY~~l~~~~~~~~~~~~~l~e~~~~L~~l~~~f 176 (199)
T PF10112_consen 126 QARKFLYYYLPTAVKLLEKYAELESQPVKSEEIKQSLEEIEETLDTLNQAF 176 (199)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHhccCCChhHHHHHHHHHHHHHHHHHHH
Confidence 3445788888899999999988776543 445566777777777776554
No 259
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=20.29 E-value=2e+02 Score=16.78 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 37 LNSFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 37 LN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
|...--.-+.|+..+++.+..||.+-.-|-.+
T Consensus 10 Lqe~~d~IEqkiedid~qIaeLe~KR~~Lv~q 41 (46)
T PF08946_consen 10 LQEHYDNIEQKIEDIDEQIAELEAKRQRLVDQ 41 (46)
T ss_dssp -----THHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHhHHHhHHHHHHHHHHHHHHHHHHHHh
Confidence 44444556677777777777777666555443
No 260
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=20.27 E-value=3.1e+02 Score=20.80 Aligned_cols=60 Identities=23% Similarity=0.330 Sum_probs=37.6
Q ss_pred HHHHHHhhhHHHHHHHHHHHh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q psy648 9 IQKQIQQDWANREYIEIITGS----IKKITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEAR 68 (72)
Q Consensus 9 v~~~iq~DW~nRe~i~~in~~----I~~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAk 68 (72)
|..-+|+-=.=+-.+..+++. +...-.=|+.|..--+++++.|...+..|++++.-.=..
T Consensus 40 Vr~lLqqy~~~~~~i~~le~~~~~~l~~ak~eLqe~eek~e~~l~~Lq~ql~~l~akI~k~~~e 103 (258)
T PF15397_consen 40 VRKLLQQYDIYRTAIDILEYSNHKQLQQAKAELQEWEEKEESKLSKLQQQLEQLDAKIQKTQEE 103 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHccChHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444333333344444333 333445588888899999999999999999888654333
No 261
>PF02994 Transposase_22: L1 transposable element; InterPro: IPR004244 Many human L1 elements are capable of retrotransposition. Some of these have been shown to exhibit reverse transcriptase (RT) activity [] although the function of many are, as yet, unknown. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 2LDY_A 3SOO_A 2YKQ_A 2YKO_C 2YKP_B 2W7A_B 2JRB_A.
Probab=20.22 E-value=1.8e+02 Score=22.53 Aligned_cols=21 Identities=48% Similarity=0.733 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy648 46 SRLAVLNEKLTTLERRIEYLE 66 (72)
Q Consensus 46 ~kLa~ln~KL~~LE~~L~~LE 66 (72)
+++..+++++..+|-+++-++
T Consensus 144 ~Ri~e~Eeris~lEd~~~~i~ 164 (370)
T PF02994_consen 144 SRIDELEERISELEDRIEEIE 164 (370)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhHHHHHHHHHHHHh
Confidence 444444444444444444333
No 262
>TIGR02169 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent.
Probab=20.19 E-value=4.6e+02 Score=22.03 Aligned_cols=38 Identities=13% Similarity=0.200 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy648 32 KITDFLNSFDMSCRSRLAVLNEKLTTLERRIEYLEARKS 70 (72)
Q Consensus 32 ~~~~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~LEAkls 70 (72)
.+..|..+.. .+..+|..++..+..++..+.-|+.++.
T Consensus 164 g~~~~~~~~~-~~~~~l~~~~~~l~el~~~~~~L~~q~~ 201 (1164)
T TIGR02169 164 GVAEFDRKKE-KALEELEEVEENIERLDLIIDEKRQQLE 201 (1164)
T ss_pred CHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555555554 5566777777777777777777666553
No 263
>PF13974 YebO: YebO-like protein
Probab=20.17 E-value=2.5e+02 Score=17.91 Aligned_cols=31 Identities=23% Similarity=0.344 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy648 35 DFLNSFDMSCRSRLAVLNEKLTTLERRIEYL 65 (72)
Q Consensus 35 ~FLN~F~~sc~~kLa~ln~KL~~LE~~L~~L 65 (72)
=|+|+++...-+-+.-|++=+++--++...|
T Consensus 16 FFVnRaSvRANEQI~LL~~ileqQKrQn~LL 46 (80)
T PF13974_consen 16 FFVNRASVRANEQIELLEEILEQQKRQNALL 46 (80)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 3799999888887777776666655555554
No 264
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=20.15 E-value=1.2e+02 Score=20.70 Aligned_cols=17 Identities=29% Similarity=0.710 Sum_probs=8.7
Q ss_pred HHHHHHHHHHHHHHhhc
Q psy648 54 KLTTLERRIEYLEARKS 70 (72)
Q Consensus 54 KL~~LE~~L~~LEAkls 70 (72)
+...+|+++.+||..|.
T Consensus 55 ~~~~~e~rI~~L~~~L~ 71 (157)
T PRK01885 55 RLREIDRRVRFLTKRLE 71 (157)
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 34445555555555554
No 265
>PF05256 UPF0223: Uncharacterised protein family (UPF0223); InterPro: IPR007920 This family of proteins is functionally uncharacterised.; PDB: 2OY9_B.
Probab=20.03 E-value=85 Score=20.30 Aligned_cols=18 Identities=28% Similarity=0.619 Sum_probs=9.1
Q ss_pred HHHhhhHHHHHHHHHHHh
Q psy648 12 QIQQDWANREYIEIITGS 29 (72)
Q Consensus 12 ~iq~DW~nRe~i~~in~~ 29 (72)
.|--||.+-|++.+++.|
T Consensus 6 Pld~dWsteEii~Vi~F~ 23 (88)
T PF05256_consen 6 PLDPDWSTEEIIDVINFF 23 (88)
T ss_dssp -------HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHH
Confidence 356799999999888754
No 266
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=20.00 E-value=1.9e+02 Score=18.57 Aligned_cols=13 Identities=38% Similarity=0.887 Sum_probs=5.5
Q ss_pred HHHHHHHHHHHHH
Q psy648 43 SCRSRLAVLNEKL 55 (72)
Q Consensus 43 sc~~kLa~ln~KL 55 (72)
.|+.+|..++.||
T Consensus 16 ~cr~~le~ve~rL 28 (85)
T PF15188_consen 16 QCRRRLEAVESRL 28 (85)
T ss_pred HHHHHHHHHHHHH
Confidence 3444444444333
Done!